Method for identifying, expanding, and removing adult stem cells and cancer stem cells

ABSTRACT

The invention further relates to means suitable for cancer treatment and even more specific for the treatment of cancer by eradicating cancer stem cells.

RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.14/494,511, filed Sep. 23, 2014, now U.S. Pat. No. 9,833,496, which is acontinuation of U.S. patent application Ser. No. 14/705,336, filed May10, 2010, now U.S. Pat. No. 8,906,631, which is a continuation ofInternational Application No. PCT/NL2008/050543, filed Aug. 8, 2008,which was published under PCT Article 21(2) in English and which claimspriority to European Application No. 07114192.3, filed Aug. 10, 2007,the entire contents of all of which are incorporated by referenceherein.

The invention relates to the fields of biochemistry, pharmacy andoncology. The invention particularly relates to the use of novel stemcell markers for the isolation of stem cells. The invention furtherrelates to the obtained stem cells and their use in for example researchor treatment, for example, for the preparation of a medicament for thetreatment of damaged or diseased tissue. The invention further relatesto means suitable for cancer treatment and even more specific for thetreatment of cancer stem cells.

Adult Stem Cells (Reviewed in 1)

Adult stem cells are found in many, if not all, organs of adult humansand mice. Although there may be great variation in the exactcharacteristics of adult stem cells in individual tissues, adult stemcells share the following characteristics: They retain anundifferentiated phenotype; their offspring can differentiate towardsall lineages present in the pertinent tissue; they retainself-maintenance capabilities throughout life; and they are able toregenerate the pertinent tissue after injury. Stem cells reside in aspecialized location, the stem cell niche. The niche typically suppliesthe appropriate cell-cell contacts and signals to maintain “sternness”.

Some tissues display a high level of steady-state turnover. Goodexamples are the hematopoietic system, the skin, and the intestinalepithelium. It is assumed that stem cells in such tissues continuouslycontribute to the self-renewal process. Other tissues, such as thebrain, the myocardium or the skeletal muscle, show very little if anyproliferative activity in steady-state situations. Stem cells in suchtissues are most likely dormant and only become active whendifferentiated cells are lost, for instance upon injury.

Bone marrow stem cells have been the subject of intensive research overthe last 30 years. Work on other adult stem cells has typically beeninitiated more recently. Good progress has been made with a limitednumber of these, i.e. the epidermal stem cell, the hair follicle stemcell, neuronal stem cells, and the mammary gland stem cell. In adramatic demonstration, a single mammary gland stem cell was shown toregenerate the entire mammary epithelium upon introduction into themammary fat pad (2).

The study of stem cells has two prerequisites:

1) It has to be possible to recognize and isolate live primary stemcells. The availability of specific (combinations of) markers isessential. As exemplified by the seminal studies in human and mouse bonemarrow, combinations of cell surface markers allow the sorting ofstrongly enriched populations of cells.2) In vitro cell culture or in vivo transplantation assays subsequentlyallow the demonstration of long-term generation of all differentiatedcell types. Typically, from these assay systems, stem cells arere-isolated and serially assayed to demonstrate long-term stemness andself-renewal.

As a non-limiting example of adult stem cells, intestinal stem cells arediscussed in more detail.

Intestinal Stem Cells

The intestinal epithelium is the most rapidly self-renewing tissue inthe adult. A handful of stem cells are believed to be located at thebase of each intestinal crypt to ensure continuous and unlimitedrenewal. Compared to the other rapidly self-renewing tissues, theintestinal stem cells have remained rather elusive. No ex vivo ortransplantation assays exist for these cells, and all knowledge ofintestinal stem cells derives from histological analysis of crypts insitu. Intestinal stem cells divide slower than their proliferatingdescendants that fill the upward positions of the crypt. While theconsensus is that colon stem cells are positioned at the bottom of thecrypts, the localization of stem cells in the small intestine remains acontroversial issue. Potten and colleagues have provided evidencesupporting a localization immediately above the Paneth cell compartmentat position +4, using the Long Term DNA label Retention assay (reviewedin 3,4). Lineage tracing studies have instigated Bjerknes and Cheng topropose that a different cell-type, the so called crypt base columnarcell, may represent the genuine stem cell. These crypt base columnarcells are intermingled with Paneth cells at the bottom-most positions ofthe crypts (5).

Only recently some candidate gene markers for intestinal stem cells havebeen proposed: i.e. Musashi (6,7) and phospho-PTEN (8). We and othersfind that the Musashi expression domain contains 30-50 cells per crypt,many more than there are stem cells (see below), while the phospho-PTENmark may represent an artifact (9).

The number of stem cells in adult crypts has been estimated between 1and 6 depending on the experimental approach used (10). It remains amatter of debate whether stemness is a set of properties that areself-perpetuated by asymmetric division through the years or whether thecrypt bottom acts as a niche that confers these properties toprogenitors residing within. The study of cell pedigrees in singlecrypts by analysis of methylation tags (11) indicates that stem cellsdivide stochastically in asymmetric (i.e. one daughter stem cell plusone differentiating progenitor) or symmetric fashion (i.e. either twostem cells daughters or two differentiating progenitors). Of note, whilethe existence of asymmetric and symmetric cell divisions is inferredfrom the above studies, no formal proof of asymmetric distribution ofdeterminants during mitosis in the intestinal epithelium has beenobserved so far.

When they reach the top third of colorectal crypts (or the villus in thesmall intestine), committed progenitors differentiate into absorbtivecells (colonocytes/enterocytes) or secretory lineage cells (gobletcells, enteroendocrine cells, Paneth cells). From this point onwards,differentiated cells continue their migration towards the villus incoherent bands stretching along the crypt-villus axis or organised atthe surface epithelium of the colorectum in clusters of hexagonalappearance. As an exception to this rule, Paneth cells migrate towardsthe crypt bottom in the small intestine (reviewed in 12).

Cancer Stem Cells (Reviewed in 13, 14)

The cancer stem cell hypothesis postulates that a small reservoir ofself-sustaining cells is exclusively able to self-renew and maintain thetumor. These cancer stem cells can expand the cancer stem cell pool, butwill also generate the heterogeneous cell types that constitute the bulkof the tumor. Cancer stem cells may be relatively refractory totherapies that have been developed to eradicate the rapidly dividingcells that constitute the bulk of a tumor. Cancer stem cells may also bethe most likely cells to metastasize. Thus, the cancer stem cellhypothesis would require that we rethink the way we diagnose and treattumors. Therapy would have to target the “minority” stem cell populationthat fuels tumor growth and metastasis, rather than the bulk of thetumor. The cancer stem cell hypothesis is at the centre of a rapidlyevolving field and may dictate changes in how basic and clinicalresearchers view cancer.

In the 1990s, studies by John Dick and others on acute myelogenousleukemia (AML) supported the existence of cancer stem cells in thisdisease (15, 16). Efforts to define the cell of origin in hematopoieticmalignancies were greatly helped by the availability of heamatopoieticlineage maps, and of cell surface markers for distinct cell types andlineages. The putative AML stem cells were demonstrated to be capable ofregenerating human AML in irradiated NOD/SCID mice. The AML stem celldisplayed a CD34⁺CD38⁻ phenotype, similar to that of normal humanhematopoietic progenitors, suggesting a close similarity between AMLstem cells and normal stem cells.

Recently, cancer stem cells have also been identified in a number ofsolid tumors. Clarke and colleagues transplanted fractioned cells fromhuman breast tumors into NOD/SCID mice. As few as a hundredCD44⁺CD24⁻/low cells could establish tumors in mice, whereas tens ofthousands of cells from different fractions failed to induce tumors(17). This example has been followed by multiple other studies on solidtumors. For instance, brain tumor stem cells that can produce seriallytransplantable brain tumors in NOD/SCID mice have been isolated fromhuman medulloblastomas and glioblastomas using the CD133 marker foundalso on normal neural stem cells (reviewed in 18). Sorting for Hoechstdye-excluding side population (SP) cells and for CD44 allowed theisolation of cancer stem cells in prostate cancer (reviewed in 19).

There is some confusion in the literature as to the definition of acancer stem cell. Here, we follow the consensus reached at a recent AACRworkshop (14), which states that the cancer stem cell “is a cell withina tumor that possesses the capacity to self-renew and to cause theheterogeneous lineages of cancer cells that comprise the tumor. Cancerstem cells can thus only be defined experimentally by their ability torecapitulate the generation of a continuously growing tumor”.Alternative terms in the literature include tumor-initiating cell andtumorigenic cell. Assays for cancer stem cell activity need to addressthe potential of self-renewal and of tumor propagation. Thegold-standard assay currently is serial xeno-transplantation intoimmunodeficient mice.

As a non-limiting example of cancer stem cells, colon cancer stem cellsare discussed in more detail.

Colon Cancer Stem Cells

Can the cancer stem cell hypothesis be extrapolated to human coloncancer? Two very recent studies imply that this is the case. John Dickand colleagues explored the usefulness of CD133 as a marker forcolorectal cancer cells (20). CD133 or Prominin, is a marker that isassociated with stem and progenitor populations in multiple tissues andcancers. They found that CD133 was expressed on 5-20% of human coloncancer cells. Subsequent serial xenograft assays demonstrated thatCD133+, but not CD133− cells could initiate tumor formation inimmunodeficient mice. It was calculated that the frequency of cancerstem cells in the isolated CD133+ population was slightly less than0.5%. Along similar lines, De Maria and colleagues found that CD133+cells comprised less than 2.5% of human colon cancer cells and alsodemonstrated that these cells could be serially transplanted intoimmunodeficient mice (21). Moreover, the CD133+ cells could bemaintained for long periods of time in culture using a serum-free mediumcontaining EGF and FGF2.

These studies imply that colon cancer may represent another example of asolid tumor in which a small number of cancer stem cells is responsiblefor maintenance of the tumor. Sorting for expression of the CD133 markerenriches significantly for the cancer stem cell, but the resulting cellmixture remains far from pure. It therefore remains unclear what theexact properties are of the cancer stem cells within the sorted cellpreparation, such as their cell cycle status, or their resistance tochemotherapy or radiation.

US 2004/0058392 and EP 1 400 807 describe a list of TCF target genesthat were defined in the colon cancer cell line Ls174T (22). In theapplications, it was speculated that these molecules expressed in coloncancer cells and in intestinal crypts would represent stem cell markers.Several of the markers encode cell-surface proteins. The inventors of US2004/0058392 and EP 1 400 807 contemplated that these proteins can beused as markers for selection of the abundant stem cell population inthe gut. However, it turned out that the overwhelming majority of theseproteins are not suitable as a stem cell selection marker as they arenot expressed (specifically) by stem cells. E.g. the CD44 protein isexpressed by all dividing crypt cells (23) as is cMyb (24) and GPX2(25). The c-Kit protein is expressed on non-dividing entero-endocrinecells (26). EphB2 is expressed by all dividing cells and EphB3 isexpressed by the non-dividing Paneth cells (27). BMP4 is expressed bystromal cells in the villus (28). And Claudin1 is expressed almostubiquitously (29).

The present invention provides markers that identify adult and/or tissuestem cells and cancer stem cells. The identified adult and/or tissuestem cells are useful in the repair of damaged or diseased tissue. Thepresent invention further provides methods that allow for the isolationof adult and/or tissue stem cells and/or cancer stem cells. Theinvention further provides ex vivo methods for culturing or maintainingor multiplying (isolated) adult and/or tissue stem cells and/or cancerstem cells. The invention yet further provides methods that allow theidentification and eradication of cancer stem cell markers. One of theobjects of the present invention is to provide novel markers that areuseful in a method for identifying adult stem cells and cancer stemcells. Another object of the present invention is to provide a methodsuitable for maintaining/culturing/multiplying/expanding adult stemcells. Yet another object of the present invention is to eradicatecancer stem cells. Adult stem cells are typically isolated from tissueand are therefore also referred to as tissue stem cells.

The surface receptors Lgr5 and Lgr 6 mark adult stem cells in multipletissues as well as cancer stem cells in multiple types of cancer. Thepresent inventors disclose that the expression patterns of the surfacemolecules Lgr5 (also known as Grp49) and of Lgr6 independently markadult stem cells in multiple tissues, as well as cancer stem cells inmultiple types of cancer. Glycoprotein hormone receptors, such as thereceptors for LH, FSH, and TSH, belong to the large G protein-coupledreceptor (GPCR) superfamily, but are unique in carrying a largeleucine-rich ectodomain important for ligand binding. These leucine-richrepeat-containing, G protein-coupled receptors in the human genome aretermed LGRs. Phylogenetic analysis shows that there are three LGRsubgroups: the known glycoprotein hormone receptors; LGR4 to 6; and athird subgroup represented by LGR7 (30). LGR5 and -6 are the mainsubject of this invention. Ligands for these two receptors remain notdescribed in the scientific literature; hence these receptors are oftenreferred to as orphans. Sequences of the human, mouse and rat receptorsare shown in FIG. 10. Human LGR4 comprises 951 amino acids, 447 of whichare identical to the corresponding amino acids in LGR5 and 485 of whichare identical to the corresponding amino acids in LGR6. Human LGR5comprises 907 amino acids, 387 of which are identical to thecorresponding amino acids in LGR6. LGR6 consists of 967 amino acids. Apredicted structure of these receptors is given in FIG. 11. LGR4/GPR48is the best studied gene of the three. According to the scientificliterature, it is broadly expressed in multiple tissues (31, 32) and notassociated specifically with stem cells. In genetic mouse models, it hasbeen described to be important for intrauterine growth (32), for malefertility (33) and for renal development (34). LGR5/GPR49 has beenknocked out. Mutant embryos die after birth due to a defect in thetongue and lower jaw (35). LGR5/GPR49 is overexpressed in hepatic andcolon cancers (22, 36, 37). LGR6 has not been studied beyond its initialcloning and sequence analysis (30).

In a first embodiment, the invention provides a method for obtaining (orisolating) adult stem cells comprising

optionally preparing a cell suspension from a normal tissue or organsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify the cells bound to said binding compound

optionally isolating the stem cells from said binding compound.

A method of the invention allows obtaining (or isolating) a collectionof cells comprising, preferably consisting of, at least 50%, morepreferred at least 60%, more preferred at least 70%, more preferred atleast 80%, most preferred at least 90% stem cells, such as between 90%and 99% stem cells or between 95% and 99% stem cells, the methodcomprising

optionally preparing a cell suspension from a normal tissue or organsample

contacting said cell suspension with an Lgr6 and/or 5 binding compound

identify or obtaining cells bound to said binding compound

optionally isolating the stem cells from said binding compound.

The isolated collection of stem cells comprises, and preferably consistsof, more than 50%, more preferred at least 60%, more preferred at least70%, more preferred at least 80%, most preferred at least 90% stemcells, such as between 90% and 99% stem cells or between 95% and 99%pure pluripotent stem cells, which can retain an undifferentiatedphenotype. The cells retain self-maintenance capabilities throughoutlife; and are able to regenerate the pertinent tissue after injury.Their offspring, or non-stem cell daughter cells, can differentiatetowards all lineages present in the pertinent tissue. Said collection ofcells can be isolated from a cell suspension comprising stem cells andnon-stem cell daughter cells such as committed or differentiateddaughter progenitor cells. An adult stem cell is preferably a stem cellobtained from a post embryonic tissue. Preferably a post natal tissue.In primates such as a human they are preferably obtained from at least ayear old subject, preferably a post-puberal subject. In a preferredembodiment of the invention said stem cells are adult stem cells and/orcancer stem cells.

A major advantage of a collection of stem cells comprising more than 50%pluripotent stem cells is that said population comprises less cells thatcan act negatively on the self maintenance capacity of the stem cellsand/or the differentiation capacity of the stem cells, compared to acollection of stem cells comprising less than 50% pure pluripotent stemcells. These negatively acting cells comprise non-stem cell daughtercells or other non-stem cells that are co-isolated with the stem cells.

Further advantages of a pure, or almost pure, population of adult stemcells are that limited cell numbers can be used as therapeutic agent forthe treatment of diseases in which the corresponding tissue has beenaffected, of which the composition is well known.

Preferably, said stem cells are tissue stem cells, such as for instanceintestinal stem cells, skin stem cells or retina stem cells. Theinvention preferably provides a method for isolating tissue stem cells,said method comprising the above described steps. Said stem cells do notinclude human embryonic stem cells. When isolating adult and/or tissuestem cells it is preferred to start with a collection of cells from thespecific tissue from which the tissue and/or adult stem cell is to beisolated. Typically a tissue stem cell and/or adult stem cell iscommitted to form cells of said tissue, however, a tissue and/or adultstem cell can exceptionally be manipulated to produce cells of anothertissue.

Stem cells are primal cells found in all multi-cellular organisms. Theyretain the ability to renew themselves through mitotic cell division andcan differentiate into a diverse range of specialized cell types. Thethree broad categories of mammalian stem cells are: embryonic cells(derived from blastocysts), adult stem cells (which are found in adulttissues) and cord blood stem cells (which are found in the umbilicalcord). The definition of a stem cell requires that it is at leastcapable of self-renewal (the ability to go through numerous cycles ofcell division while maintaining the undifferentiated state) and has anunlimited potency (the capacity to differentiate into any mature celltype, i.e. being either totipotent, pluripotent, multipotent orunipotent).

In a preferred embodiment, the invention provides a method for obtaining(or isolating) stem cells comprising

optionally preparing a cell suspension from a normal tissue sample

contacting said cell suspension with an Lgr 5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the stem cells from said binding compound, whereinsaid stem cells are adult stem cells, more preferably mammalian adultstem cells and even more preferably human adult stem cells. These adultstem cells typically act as a repair system for the body and arereplenishing specialized cells. Adult stem cells are found in childrenas well as in adults and most adult stem cells are lineage restricted(multipotent) and are referred to by their tissue origin, for exampleskin stem cell or retina stem cell.

A tissue or organ sample can be obtained via any known method, such as abiopsy. Moreover, a tissue or organ sample can be obtained from anypossible tissue or organ, such as, but not limited to, heart, retina,breast, ovary, lung, brain, eye, stomach, pancreas, liver, intestinecomprising colon and rectal tissue, skin, hair follicle, and adrenalmedulla,

The phrase “a normal tissue or organ sample” is used herein to refer toa tissue or organ sample which is healthy, non-transformed,non-malignant, non-cancerous or non-tumorigenic, i.e. a healthy,non-transformed, non-malignant, non-cancerous or non-tumorigenic tissueor organ sample. Any pathologist, skilled in the art, can determine if atissue is healthy non-transformed, non-malignant, non-cancerous, ornon-tumorigenic.

In a preferred embodiment, the used tissue or organ sample is ofmammalian human origin. Even more preferably, the tissue is adult tissue(i.e. tissue of a borne mammal, i.e. non-embryonic/fetal tissue).

Bone marrow and (cord) blood can be considered natural cell suspensions.From solid organs, cell suspensions can be obtained for instance bymechanical disruption of organ tissue into small fragments. Thesefragments can then optionally be further segregated into single cells bychemicals such as EDTA and/or by enzymatic digestion with for instancethe enzyme preparations trypsine, dispase, collagenase or pancreatin.The procedure can involve tissue or cell culture before, during or afterthe disruption and/or enzymatic digestion procedures

As it is not always necessary to isolate the stem cells from the usedbinding compound, said step is presented as an optional feature in theclaim. When it is necessary to isolate the stem cells from the Lgr 5and/or 6 binding compound, this can be performed by multiple methodswell known to the skilled person. Suitable examples are (mechanical)agitation, enzymatic digestion, addition of excess binding compound or aderivative thereof, elution by changing pH or salt concentration.

Now that the inventors have provided evidence that Lgr5 or 6 are(unique) markers for stem cells, compounds that are capable of bindingto Lgr5 and/or 6 (i.e. Lgr5 or 6 binding compounds) can be used toidentify, mark and isolate stem cells.

One suitable example of an Lgr5 or 6 binding compound is an antibody oran antibody derivative or an antibody fragment capable of binding toLgr5 or 6, i.e. an antibody or derivative or fragment thereof that hasaffinity for Lgr5 or 6. As Lgr5 and 6 are transmembrane surfaceproteins, such an antibody or a derivative or a fragment thereofpreferably has affinity for the part of the protein facing externally,i.e. binds to any extracellular part. In a preferred embodiment, saidantibody or an antibody derivative or an antibody fragment has a highaffinity for Lgr5 and/or 6.

Hence, in a preferred embodiment, the invention provides a method forobtaining (or isolating) stem cells comprising

optionally preparing a cell suspension from a normal tissue or organsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the stem cells from said binding compound, whereinsaid Lgr5 and/or 6 binding compound is an antibody or an antibodyderivative or an antibody fragment capable of binding to Lgr5 and/or 6.

Antibodies or their derivatives and/or their fragments can be providedby methods that are well known to the person skilled in the art andinclude the hybridoma technology in normal or transgenic mice or inrabbits, or phage display antibody technology. In one embodiment,genetic immunization is used. This technique comprises administration ofa nucleic acid sequence, or a functional equivalent thereof, encoding atleast one antigen of interest, to a non-human animal. The encodedantigen(s) is/are produced by the animal, which stimulates the animal'simmune system against said antigen(s). Hence, an immune response againstsaid antigen(s) is elicited in said animal. Subsequently, T-cells,B-cells and/or antibodies specific for an antigen of interest arepreferably obtained from said animal. Said T-cells, B-cells and/orantibodies are optionally further processed. In one preferredembodiment, an obtained B-cell of interest is used in hybridomatechnology wherein said obtained B-cell is fused with a tumor cell inorder to produce a hybrid antibody producing cell.

Examples of suitable antibody fragments are scFv, Fab, or (Fab)2fragments. Examples of suitable derivatives are chimeric antibodies,nanobodies, bifunctional antibodies or humanized antibodies.

In yet another preferred embodiment, the used antibody is a monoclonalantibody.

In a further preferred embodiment, a Lgr5 and/or 6 binding compoundcomprises an antibody or an antibody derivative or an antibody fragmentcomprising a heavy chain CDR1, CDR2 and/or CDR3 sequence as depicted inFIG. 27, and preferably also comprising a complementary immunoglobulinlight chain molecule, whereby the CDR sequences are determined accordingto Kabat (Kabat et al., “Sequences of Proteins of ImmunologicalInterest,” U.S. Dept. of Health and Human Services, National Instituteof Health, 1987). Preferably, said antibody or antibody derivative orantibody fragment comprises the heavy chain CDR1 sequence and the heavychain CDR2 sequence and the heavy chain CDR3 sequence of a heavy chainas depicted in FIG. 27. It was found by the inventors that an antibodyor an antibody derivative or an antibody fragment, such as for example ascFv, Fab, or (Fab)2 fragment, comprising a heavy chain CDR1, CDR2and/or CDR3 sequence as depicted in FIG. 27 constitutes a high affinitybinding compound with a high specificity for their target proteins.

In a further preferred embodiment, a Lgr5 and/or 6 binding compoundcomprises an antibody or an antibody derivative or an antibody fragmentcomprising a light chain CDR1, CDR2 and/or CDR3 sequence as depicted inFIG. 27, and preferably also comprising a complementary immunoglobulinheavy chain molecule, whereby the CDR sequences are determined accordingto Kabat (Kabat et al., “Sequences of Proteins of ImmunologicalInterest,” U.S. Dept. of Health and Human Services, National Instituteof Health, 1987). Preferably, said antibody or antibody derivative orantibody fragment comprises the light chain CDR1 sequence and the lightchain CDR2 sequence and the light chain CDR3 sequence of the light chainas depicted in FIG. 27. It was found by the inventors that an antibodyor an antibody derivative or an antibody fragment, such as for example ascFv, Fab, or (Fab)2 fragment, comprising a light chain CDR1, CDR2and/or CDR3 sequence as depicted in FIG. 27 constitutes a high affinitybinding compound with a high specificity for their target proteins.

In one preferred embodiment, a Lgr5 and/or 6 binding compound comprisesan antibody as depicted in Table 4 or 5.

A method according to the invention, wherein an antibody as depicted inTable 4 or 5 is used is therefore also herewith provided, as well as amethod according to the invention, wherein an antibody or an antibodyderivative or an antibody fragment is used which comprises at least oneCDR sequence as depicted in FIG. 27. Preferably, said antibody orantibody derivative or antibody fragment comprises a CDR1 sequence and aCDR2 sequence and a CDR3 sequence of a light chain and/or heavy chaindepicted in FIG. 27.

In a specific embodiment, a binding compound comprising a heavy chainand/or a light chain CDR1, CDR2 and/or CDR3 sequence as depicted in FIG.27, is a rat monoclonal antibody. In preferred embodiment, a bindingcompound comprising a heavy chain and/or a light chain CDR1, CDR2 and/orCDR3 sequence as depicted in FIG. 27, is a chimaeric, deimmunized, orhumanized monoclonal antibody. Methods for generating a chimaeric,deimmunized, or humanized monoclonal antibody or derivative or fragmentthereof comprising a heavy chain and/or a light chain CDR1, CDR2 and/orCDR3 sequence as depicted in FIG. 27, are known in the art. For example,a chimaeric antibody can be generated comprising a rodent variableregion comprising the indicated CDR sequence(s) fused to a non-rodent,for example a human, constant region (Morrison et al. 1984. Proc NatlAcad Sci USA 81: 6851-6855; which is hereby incorporated by reference).Methods for deimmunization of a binding compound comprising a heavychain and/or a light chain CDR1, CDR2 and/or CDR3 sequence as depictedin FIG. 27 are also known to a skilled person, for example fromGiovannoni, 2003. Neurology 61: S13-S17; which is hereby incorporated byreference. Humanization of a non-human antibody is principally achievedthrough grafting of the CDR regions to a human immunoglobulin frameworkregion as is shown, for example, in U.S. Pat. Nos. 6,548,640, 5,530,101,and 5,859,205, which are all hereby incorporated by reference.

A human antibody against Lgr5 or 6 can also be generated in an animalprovided with human sequences encoding an immunoglobulin heavy and/orlight chain gene such as transgenic strains of mice in which mouseantibody gene expression is suppressed and effectively replaced withhuman antibody gene expression. Examples are provided by theHuMAb®-Mouse technology of Medarex; the TC Mouse™ technology of Kirin,and the KM-Mouse® technology, a crossbred mouse that combines thecharacteristics of the HuMAb-Mouse with the TC Mouse.

The invention further provides the use of a binding compound accordingto the invention for identifying or isolating stem cells from apopulation of cells comprising stem cells and committed ordifferentiated daughter progenitor cells; whereby the isolated stemcells comprise at least 50% pure pluripotent stem cells.

Another example of an Lgr5 or 6 binding compound is an Lgr5 or 6 ligand.Such an Lgr5 or 6 ligand can be used unmodified, can be produced and/orused as a fusion protein (i.e. a ligand fusion protein) or can becoupled to a second moiety to, for example, allow cell separation.

In a preferred embodiment, the invention therefore provides a method forobtaining (or isolating) stem cells comprising

optionally preparing a cell suspension from a normal tissue or organsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the stem cells from said binding compound, whereinsaid Lgr5 and/or 6 binding compound is a Lgr5 or 6 ligand, for example aligand fusion protein.

The person skilled in the art is very well capable of producing an Lgr5or 6 ligand fusion protein, for example via standard molecular biologytechniques.

A suitable example of an Lgr5 or 6 ligand is a member of the insulinpeptide family, such as Ins15 or relaxin3. Another suitable example is acysteine-knot protein such as Noggin, Gremlin1 or -2, Dan, or Cerberus.The nucleotide and amino acid sequences of these ligands are known andthe skilled person is thus for example capable to produce a ligandfusion protein.

Preferably the second moiety of a ligand fusion protein introduces afeature which allows for easy identification and tracing of the fusionprotein, for example a protein (fragment) such as the antibody Fc tailor Staphylococcal protein A or Glutathion-S-transferase, a shortantigenic peptide tag such as the Myc, FLAG or HA tag or an oligomericHistidine-tag, an enzymatic tag such as Alkaline Phosphatase, afluorescent protein tag such as Green Fluorescent Protein. Smallchemical moieties can also be coupled to the ligand for stem cellidentification and/or isolation. These moieties can be recognized andbound by specific antibodies, or can have specific affinity for amaterial to be used in cell separation, or can for instance befluorescent. In an even more preferred embodiment, the second part ofthe fusion protein is linked to an Lgr5 or 6 ligand via a spacer. Evenmore preferable, said spacer comprises an enzyme digestible sequence.This allows for an easy separation of the second moiety and the Lgr5 or6 ligand.

Yet another example of an Lgr5 or 6 binding compound is a small compoundthat has affinity for Lgr5 or 6.

In a preferred embodiment, the invention thus provide a method forobtaining (or isolating) stem cells comprising

optionally preparing a cell suspension from a normal tissue or organsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the stem cells from said binding compound,

wherein said Lgr5 or 6 binding compound is a small molecule withaffinity for Lgr5 or 6. A suitable example is a small chemical moleculeor a small non-chemical molecule or a small protein.

In a preferred embodiment, the affinity of said small molecule for Lgr5or 6 is a high affinity, i.e. an affinity with a Kd of at least 10⁻⁷.

As already outlined above, the invention provides a method for obtaining(or isolating) stem cells comprising

optionally preparing a cell suspension from a normal tissue or organsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the stem cells from said binding compound,

wherein said cells are preferably (adult) (tissue) stem cells.

Non-limiting examples of stem cells that can be obtained via the abovementioned methods are skin, intestinal comprising colon and rectal, eye,retina, brain, breast, hair follicle, pancreas, stomach, liver, lung,heart, adrenal medulla, or ovarian stem cells. It has not beenpreviously been possible to obtain or isolate stomach, intestinal orretina stem cells. Hence, in a preferred embodiment, the obtained orisolated stem cells are stomach, intestinal or retina stem cells.

Depending on the desired adult and/or tissue stem cell and the presenceor absence of Lgr5 and/or 6, a method according to the invention can beperformed with at least one, at least two, at least three or even more(different) binding compound(s). Table 1 provides an overview of thepresence or absence of Lgr5 or 6 on different kind of adult and/ortissue stem cells. Based on Table 1 the person skilled in the art isvery well capable of selecting one or multiple target markers and one ormultiple corresponding binding compounds and to obtain or isolate stemcells from a particular normal tissue or organ.

TABLE 1 The distribution of the adult and/or tissue stem cell markersLgr5 and 6 marker stem cell Lgr5 Lgr6 brain + + kidney − − liver + −lung − + retina + − stomach + − intestine + − pancreas + − testis − −breast + + hair follicle + + heart − + ovary + − adrenal medulla + −skin + + bladder + − bone + − connective tissue + + ear + − muscle + −prostate + − placenta + − uterus + + bone marrow − + eye − +

If the person skilled in the art wants, for example, to obtain breaststem cells, a binding compound of Lgr5 or 6 can be used alone or in anycombination thereof, because the breast stem cells comprise both of saidmarkers.

In a preferred embodiment, the invention provides a method for obtaining(or isolating) stem cells comprising

optionally preparing a cell suspension from a normal tissue or organsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the stem cells from said binding compound,

wherein

-   -   said Lgr5 and/or 6 binding compound is an Lgr5 binding compound        and wherein said stem cells are brain, liver, retina, stomach,        intestine, pancreas, ovary, hair follicle, adrenal medulla,        skin, bladder, bone, ear, muscle, prostate, placenta, or breast        stem cells; or    -   said Lgr5 and/or 6 binding compound is an Lgr6 binding compound        and wherein said stem cells are brain, skin, lung, breast, hair        follicle, bone marrow, eye, or heart stem cells; or    -   said Lgr5 and/or 6 binding compound is at least one Lgr6 binding        compound in combination with at least one Lgr5 binding compound        and wherein said stem cells are brain, breast, skin, connective        tissue, uterus, or hair follicle stem cells.

In yet another preferred embodiment, the invention provides a method forobtaining (or isolating) stem cells comprising

optionally preparing a cell suspension from a normal tissue or organsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the stem cells from said binding compound,

wherein said stem cell is any of the stem cells identified in Table 1and wherein the used Lgr5 and/or 6 binding compound corresponds to thedesired stem cell as shown in Table 1, with the proviso that in case thestem cell is an intestinal or hair follicle cell, the Lgr5 or 6 bindingcompound is not uniquely targeting Lgr5 (i.e. is not a Lgr5 bindingcompound alone).

In a preferred embodiment, the invention provides a method for obtaining(or isolating) stem cells comprising

-   -   optionally preparing a cell suspension from a normal tissue or        organ sample    -   contacting said cell suspension with an Lgr5 and/or 6 binding        compound    -   identify or obtaining the cells bound to said binding compound    -   optionally isolating the stem cells from said binding compound,        wherein one binding compound is used.

In yet another preferred embodiment, the invention provides a method forobtaining (or isolating) stem cells comprising

-   -   optionally preparing a cell suspension from a normal tissue or        organ sample    -   contacting said cell suspension with an Lgr5 and/or 6 binding        compound    -   identify or obtaining the cells bound to said binding compound    -   optionally isolating the stem cells from said binding compound,        wherein at least two different binding compounds are contacted        with said cell suspension. Said two different binding compounds        can be directed against one and the same marker (i.e. directed        to Lgr5 or to Lgr6). For example use can be made of two        antibodies directed to two different epitopes which antibodies        together provide (a preferably essentially complete) capture of        the desired stem cells. However, said two different binding        compounds can also be directed to two different stem cell        markers (i.e. one binding compound for Lgr5 and one for Lgr6).        Whenever use is made of two or three or even more binding        compounds, said binding compounds may be from the same class of        binding compounds (for example all being antibodies, small        molecules or ligand fusion proteins) or may be from different        classes of binding compounds (for example an antibody directed        to Lgr6 and a ligand fusion protein for binding to Lgr5).

In a preferred embodiment, at least two different antibodies or antibodyderivatives or antibody fragments capable of binding to Lgr5 or 6 arecontacted with a cell suspension.

After allowing the binding compounds to interact with the cellsuspension (for a certain amount of time or under different conditionssuch as pH, temperature, salt etc.), subsequent identification ofobtained bound complexes is performed. This is for example accomplishedby using FACS analysis. Fluorescence-activated cell-sorting (FACS) is aspecialised type of flow cytometry. It provides a method for sorting aheterogeneous mixture of biological cells into two or more containers,one cell at a time, based upon the specific light scattering andfluorescent characteristics of each cell. It is a useful scientificinstrument as it provides fast, objective and quantitative recording offluorescent signals from individual cells as well as physical separationof cells of particular interest.

In a preferred embodiment, the invention provides a method for obtaining(or isolating) stem cells comprising

-   -   optionally preparing a cell suspension from a normal tissue or        organ sample    -   contacting said cell suspension with an Lgr5 and/or 6 binding        compound    -   identify or obtaining the cells bound to said binding compound    -   optionally isolating the stem cells from said binding compound,        wherein a FACS is used to identify and sort the cells that bind        to an Lgr5 or 6 binding compound.

Other options for isolation of stem cells utilizes binding compoundsbound to Lgr5 or 6 on stem cells in conjunction with magnetic beadsorting, immunoaffinity column cell separation or panning.

For analysis by FACS, the binding compound is provided with afluorescence label, for analysis by magnetic bead sorting the bindingcompound is provide with magnetic beads (for example an antibody-coatedmagnetic bead), for immunoaffinity it is bound to a solid support, forpanning to tissue culture dishes.

Now that we know that Lgr5 and/or 6 are markers for adult stem cells,this knowledge can also be used in respect of the culturing of adultstem cells. Ligands of Lgr5 and/or 6 as well as small molecule agonistsof Lgr5 and/or 6 can be used as a stimulator for the growth of normal(i.e. healthy, non-transformed, normal) adult stem cells.

The invention therefore also provides a method for maintaining orculturing tissue or organ stem cells, comprising providing tissue ororgan stem cells with an Lgr5 and/or 6 ligand or a small moleculeagonist of Lgr5 and/or 6.

The term “maintaining” is used herein to describe the situation in whichthe number of stem cells is essentially not changed. The term“culturing” is used herein to describe the situation in which the amountof stem cells is increased, i.e. in which the cells are expanded whileretaining their stem cell phenotype.

After the tissue or organ stem cells have been provided with an Lgr5and/or 6 ligand, the cells are incubated in tissue culture atcircumstances (temperature, culture medium, pH) that allow formaintenance or expansion.

The stem cells can be obtained via any suitable method but arepreferably obtained by any of the methods described herein, i.e. amethod for obtaining (or isolating) stem cells comprising

optionally preparing a cell suspension from a normal tissue or organsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the stem cells from said binding compound.

In a preferred embodiment, the invention provides a method formaintaining or culturing tissue or organ stem cells, comprisingproviding tissue stem cells with an Lgr5 and/or 6 ligand or a smallmolecule agonist of Lgr5 and/or 6, wherein said ligand is a member ofthe insulin peptide family. A suitable example of an Lgr5 or 6 ligand isa member of the insulin peptide family, such as Ins15 or relaxin3.Another suitable example is a cysteine-knot protein such as Noggin,Gremlin 1 or 2, Dan, or Cerberus.

The invention further provides (isolated) stem cells, or a collection ofisolated stem cells, preferably from mammalian origin and even morepreferably human stem cells or human adult stem cells, wherein at least50% of the cells are Lgr5 or 6 positive, pluripotent stem cells.Preferably, at least 60% of the cells are Lgr5 or 6 positive,pluripotent stem cells. More preferably, at least 70% of the cells areLgr5 or 6 positive, pluripotent stem cells. More preferably, at least80% of the cells are Lgr5 or 6 positive, pluripotent stem cells. Morepreferably, at least 90% of the cells are Lgr5 or 6 positive,pluripotent stem cells. Most preferably, at least 95% of the cells areLgr5 or 6 positive, pluripotent stem cells. The purity of the collectioncan be increased as indicated herein above. In a preferred embodimentthe invention provides (isolated) stem cells or a collection of isolatedstem cells wherein said stem cells contain bound specific Lgr5 and/orLgr6 binding compound. Preferably a specific Lgr5 and/or Lgr6 bindingantibody as described herein above or a fragment or derivative thereof.The invention further provides a culture of stem cells comprising abinding antibody specific for Lgr5 and/or Lgr6 or a specific fragment ofat least 20 amino acids of said Lgr5 and/or Lgr6 binding antibody.

In a preferred embodiment, said stem cells are, or said collection ofstem cells comprises, brain, liver, retina, stomach, intestine includingcolon and rectal, ovary, hair follicle, adrenal medulla, skin, bladder,bone, connective tissue, ear, muscle, prostate, placenta, uterus, orbreast stem cells that comprise Lgr5 in their cell membrane.

In a particularly preferred embodiment, said stem cells are, or saidcollection of stem cells comprises, brain, lung, skin, breast, hairfollicle, connective tissue, uterus, bone marrow, eye, or heart stemcells that comprise Lgr6 in their cell membrane.

In a further preferred embodiment, said stem cells are, or saidcollection of stem cells comprises, brain, breast, skin, connectivetissue, uterus, or hair follicle stem cells that comprise Lgr5 as wellas Lgr6 in their cell membrane.

In yet another embodiment, the invention provides stem cells, or acollection of stem cells wherein at least 50%, preferably at least 60%,more preferably at least 70%, more preferably at least 80%, morepreferably at least 90%, more preferably at least 95% of the cells areLgr5 or 6 positive, pluripotent stem cells, obtainable by a methodaccording to the invention, i.e.

(i) a method for obtaining (or isolating) stem cells comprising

optionally preparing a cell suspension from a normal tissue or organsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the stem cells from said binding compound, and/or

(ii) a method for maintaining or culturing tissue stem cells, comprisingproviding tissue stem cells with an Lgr5 and/or 6 ligand or a smallmolecule agonist of Lgr5 and/or 6.

The stem cells, or the collection of stem cells, isolated according tothe invention can be used as a therapeutic agent for the treatment ofdiseases in which the corresponding tissue has been affected. However,the obtained stem cells are also very useful for other purposes.

In yet another useful embodiment, the invention provides the use of stemcells, or a collection of stem cells, as obtained by any of the hereindescribed methods, in the preparation of a medicament for treatingdamaged or diseased tissue.

Preferably said stem cells are human stem cells. Even more preferablythe acceptor is human as well. Table 2 provides an overview of differentstem cells and the diseases in which they can therapeutically be used.

TABLE 2 Therapeutic applications for use of Lgr5⁺ and/or Lgr6⁺ stemcells stem cell Therapeutic application brain Brain damage such asstroke and traumatic brain injury. Degenerative diseases such asAlzheimer's, Parkinson, Huntington's kidney Chronic or acute kidneyfailure liver Chronic liver failure, for instance due to damage byinfectious agents, chemicals including alcohol or metabolic disorderslung COPD, fibrosis retina Blindness and vision impairments due todefects in the retina stomach Pernicious anemia Intestinal, Crohn'sdisease, tissue damage resulting from colon, rectal, and chemotherapy orother toxic agents, colorectal pancreas Diabetes testis Sterility breastBreast reconstruction hair follicle Baldness heart Heart disease such ascongestive heart failure ovary Sterility Skin Skin grafting Adrenalmedulla Addison's Disease

Hence, the invention provides a use of stem cells, or a collection ofstem cells, as obtained by any of the herein described methods, in thepreparation of a medicament for treating damaged or diseased tissue,

wherein said stem cells are intestinal stem cells and wherein saidtissue is damage to the intestinal epithelium, damage to the liver ordamage to the pancreas or

wherein said stem cells are retina stem cells and wherein tissue damageis damaged retina; such an approach is useful in the treatment ofblindness due to defects in the retina; or

wherein said stem cells are brain stem cells; or

wherein said stem cells are breast stem cells; or

wherein said stem cells are hair follicle stem cells and the damagestissue are hair follicles; such an approach is extremely useful in thetreatment of baldness and involves isolating of follicle stem cells bythe herein described method, multiplying the obtained stem cells andimplanting the new follicles into the scalp; or

wherein said stem cells are stomach stem cells; or

wherein said stem cells are liver stem cells; or

wherein said stem cells are ovarian stem cells; or

wherein said stem cells are skin stem cells for providing skin grafts;or

wherein said stem cells are any of the cells mentioned in Table 2 andthe disease to be treated is mentioned as the corresponding therapeuticapplication in Table 2, for example the stem cells are retina stem cellsand the disease is blindness due to defects in the retina.

Gene therapy can additionally be used in a method directed at repairingdamaged or diseased tissue. Use can, for example, be made of anadenoviral or retroviral gene delivery vehicle to deliver geneticinformation (like DNA and/or RNA) to stem cells. A skilled person canreplace or repair particular genes targeted in gene therapy. Forexample, a normal gene may be inserted into a nonspecific locationwithin the genome to replace a nonfunctional gene. This approach iscommon. In yet another example, an abnormal gene could be swapped for anormal gene through homologous recombination or an abnormal gene couldbe repaired through selective reverse mutation, which returns the geneto its normal function. A further example is altering the regulation(the degree to which a gene is turned on or off) of a particular gene.Preferably, the stem cells are ex vivo treated by a gene therapyapproach and are subsequently transferred to the mammal (preferably ahuman being) in need of treatment.

Thus, the invention also provides a method for modifying a genomicsequence of a stem cell, comprising providing a collection of stem cellsaccording to a method of the invention, contacting said collection witha nucleic acid to modify a genomic sequence, and isolating a stem cellin which a genomic sequence has been modified. The invention furtherprovides a method for modifying a genomic sequence of a tissue cellcomprising providing a collection of tissue cells in vitro with anucleic acid sequence for modifying said genomic sequence, furthercomprising isolating a stem cell from said collection of tissue cellsaccording to a method of the invention.

The invention further provides isolated, genomicly modified stem cellsobtainable by a method of the invention, and wherein at least 50%,preferably at least 60%, more preferably at least 70%, more preferablyat least 80%, more preferably at least 90%, more preferably at least 95%of the cells are pluripotent stem cells which can retain anundifferentiated phenotype. The invention further provides isolated,genomicly modified stem cells obtainable by a method of the invention,and wherein at least 50%, preferably at least 60%, more preferably atleast 70%, more preferably at least 80%, more preferably at least 90%,more preferably at least 95% of the cells are adult and/or tissue stemcells as defined herein.

In yet another useful embodiment, the invention provides the use of stemcells as obtained by any of the herein described methods, in thepreparation of a medicament for treating damaged or diseased tissue,further comprising genetically modifying said stem cells preferably exvivo and/or preferably by a gene therapy approach. The invention furtherprovides a composition for treating tissue or organ damage comprisingisolated genomicly modified stem cells according to the invention.

In yet an alternative embodiment, the invention provides a compositionfor treating tissue damage comprising tissue stem cells obtainable by amethod according to the invention, i.e.

(i) a method for obtaining (or isolating) stem cells comprising

optionally preparing a cell suspension from a tissue or organ sample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the stem cells from said binding compound, and/or

(ii) a method for maintaining or culturing tissue stem cells, comprisingproviding tissue stem cells with an Lgr5 and/or 6 ligand or a smallmolecule agonist of Lgr5 and/or 6.

Stem cells of the invention are also very useful for research purposes.Examples of suitable research purposes are further identification ofstem cell markers or the development of gene therapy with the stem cellsof the invention as a target or any other research purpose.

The invention further provides a use of Lgr5 and/or 6 as a marker forthe isolation of tissue stem cells as well as the use of an Lgr5 and/or6 binding compound for the isolation of tissue stem cells.

The invention further provides a method for treating an individual inneed thereof comprising administering to said individual a sufficientamount of stem cells obtainable/obtained by a method according to theinvention.

In a further embodiment, the invention provides a recombinant animalcomprising a first reporter gene under control of a Lgr5 or Lgr6promoter such that the reporter gene product is expressed in cellsexpressing Lgr5 or Lgr6, a sequence encoding a regulatable protein beingin an operable linkage with the first reporter gene such that theregulatable protein is co-expressed with the first reporter gene productin cells expressing Lgr5 or Lgr6, and a second reporter gene that isexpressed upon activation of the regulatable protein.

A recombinant animal of the invention allows staining of tissue or organstem cells with said first reporter, and allows staining of non-stemcells daughter cells such as committed or differentiated daughterprogenitor cells with the second reporter gene product after activationof the regulatable protein.

A reporter gene is a gene that encodes a product that can readily beassayed. Reporter genes are typically used to determine whether aparticular nucleic acid construct has been successfully introduced intoa cell, organ or tissue and/or to specifically detect the cell in whichthe reporter gene has been introduced and is expressed. The expressionproduct is typically unique in the sense that non modified cells orcells that do not express the reporter gene are not specificallydetected. A reporter gene is also referred to as a marker gene. When twoor more reporter genes are used, the different reporter genes aretypically not the same, in the sense that their expression products caneasily be distinguished from each other. Thus a first and a secondreporter gene are typically not the same. A regulatable protein as usedherein is a protein that, upon the presence of a signal, alters itsfunction. Many different regulatable proteins have been identifiedand/or artificially generated. A well known example is the tet-repressorsystem where the presence or absence of tetracycline or an analoguethereof regulates the activity of the tet-operon by regulating thebinding capacity of the tet-repressor protein to the tet-repressorbinding sequence. In this example the tet-repressor protein is theregulatable protein and the presence or absence of tetracycline is thesignal. Although the tet-repressor system is well known, there are manyother regulatable proteins.

Co expression of two or more proteins in a cell is currently verycommon. Fusion proteins can be generated. Preferably a multi-cistron isused. This is currently typically achieved using at least one so-calledinternal ribosomal entry site (IRES). Alternative methods include theuse of reinitiation sites and/or alternative splicing of an RNAcontaining two or more open reading frames.The invention also provides a recombinant stem cell comprising a firstreporter gene under control of a Lgr5 or Lgr6 promoter such that thereporter gene product is expressed in cells expressing Lgr5 or Lgr6, asequence encoding a regulatable protein being in an operable linkagewith the first reporter gene such that the regulatable protein isco-expressed with the first reporter gene product in cells expressingLgr5 or Lgr6, and a second reporter gene that is expressed uponactivation of the regulatable protein.

Said stem cell can be generated from an isolated stem cell, orpreferably is isolated from a recombinant animal according to theinvention.

Said regulatable protein preferably is CRE-ERT2, which can be activatedby administration of an estrogen or analogue thereof such as tamoxifenor 4-hydroxytamoxifen. In this preferred embodiment, the expression ofthe second reporter gene is regulated by activated CRE-ERT2 through theremoval of a repressor sequence that prevents expression of the secondreporter gene in the inactive state. In a preferred embodiment, saidfirst reporter gene product is a fluorescent protein such as greenfluorescent protein, or more preferred enhanced green fluorescentprotein. In a further preferred embodiment, said second reporter genecomprises LacZ, encoding beta-galactosidase which can be identifiedthrough provision of a suitable substrate such as X-gal. Said secondreporter gene is preferably inserted into a genomic region that providesrobust, prolonged expression of the transgene after activation, such asthe ROSA locus if the transgenic animal is a mouse.

In a preferred embodiment the invention provides a recombinant animalcomprising the nucleic acids as specified in the examples in the contextof the recombinant animal for tracing stem cells described therein.

In a preferred embodiment said recombinant animal is a non-human animal.Preferably a mammal, more preferably a rodent. More preferably a rat ora mouse.

The invention further provides the use of a recombinant animal or arecombinant stem cell according to the invention for tracing stem cellsand descendants of a stem cell.

The invention also provides a method for identifying descendants of astem cell, comprising providing a recombinant animal or recombinant stemcell according to the invention, activating the regulatable protein, andidentifying cells that do not express Lgr5 and/or 6 and the firstreporter, and express the second reporter protein.

The present inventors disclose that the expression of Lgr5 (also knownas Grp49) as well as the expression of Lgr6 not only mark adult stemcells, but also mark cancer stem cells in multiple different tumors.

In yet another embodiment, the invention provides a method for obtaining(or isolating) cancer stem cells comprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound.

Preferably said cancer stem cells are involved in intestinal cancer,including colon, rectal and colorectal cancer, skin cancer such as basalcell carcinoma, esophageal cancer, breast cancer, prostate cancer,medulloblastoma and other brain cancers, liver cancer, stomach cancer,retina, head and neck cancer, testicular cancer, hair follicle, ovariancancer, adrenal medulla cancer (pheochromocytoma) or lung cancer. Thus,in a preferred embodiment, said cancer stem cells are intestinal cancerstem cells, including colon-, rectal- and colorectal cancer stem cells,skin cancer stem cells such as basal cell carcinoma stem cells,esophageal cancer stem cells, breast cancer stem cells, prostate cancerstem cells, medulloblastoma stem cells and other brain cancer stemcells, liver cancer stem cells, stomach cancer stem cells, retina stemcells, head and neck cancer stem cells, testicular cancer stem cells,hair follicle cancer stem cells, ovarian cancer stem cells,pheochromocytoma stem cells, or lung cancer stem cells.

As mentioned, there is some confusion in the literature as to thedefinition of a cancer stem cell. Herein, we follow the consensusreached at a recent AACR workshop (14), which states that the cancerstem cell “is a cell within a tumor that possesses the capacity toself-renew and to cause the heterogeneous lineages of cancer cells thatcomprise the tumor. Cancer stem cells can thus only be definedexperimentally by their ability to recapitulate the generation of acontinuously growing tumor”. Alternative terms in the literature includetumor-initiating cell and tumorigenic cell. Assays for cancer stem cellactivity preferably need to address the potential of self-renewal and oftumor propagation. The gold-standard assay currently is serialxeno-transplantation into immunodeficient mice.

A solid tumor sample is for example obtained via biopsy or surgicaltechniques and a liquid tumor sample is for example obtained by taking ablood, urine, cerebrospinal fluid or lymph sample from a mammal,preferably a human.

The tissue or organ that is sampled is for example the colon, a breast,prostate, brain, liver, stomach or lung.

For information in respect of Lgr5 or 6, the earlier parts of thisapplication can be considered.

In a preferred embodiment, the invention provides a method for obtaining(or isolating) cancer stem cells, or a collection of cancer stem cells,comprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound,

wherein said cancer stem cells are mammalian, preferably human, cancerstem cells, and wherein the collection of cancer stem cells comprises atleast 50% cancer stem cells that are able to recapitulate the generationof a continuously growing tumor. In a preferred embodiment saidcollection of cancer stem cells comprises at least 60% cancer stemcells, preferably at least 70% cancer stem cells, more preferably 80%cancer stem cells, more preferably 90% cancer stem cells, morepreferably 95% cancer stem cells that are able to recapitulate thegeneration of a continuously growing tumor.

Bone marrow and (cord) blood can be considered natural cell suspensions.From solid tumors, cell suspensions can be obtained for instance bymechanical disruption of organ tissue into small fragments. Thesefragments can then optionally be further segregated into single cells bychemicals such as EDTA and/or by enzymatic digestion with for instancethe enzyme preparations dispase, collagenase or pancreatin. Theprocedure can involve tissue or cell culture before, during or after thedisruption and/or enzymatic digestion procedures.

When a cell suspension is already available this step of the method canbe omitted (optional feature).

As it is not always necessary to isolate the cancer stem cells from theused binding compound, said step is presented as an optional feature inthe claim. When it is necessary to isolate the cancer stem cells fromthe Lgr5 or 6 binding compound, this can be performed by multiplemethods well known to the skilled person. Suitable examples are(mechanical) agitation, enzymatic digestion, addition of excess bindingcompound or a derivative thereof, elution by changing pH or saltconcentration.

Now that the inventors have shown that Lgr5 or 6 are markers for cancerstem cells, compounds that are capable of binding to Lgr5 or 6 (i.e.Lgr5 or 6 binding compounds) can be used to identify, mark and isolatecancer stem cells.

One suitable example of an Lgr5 or 6 binding compound is an antibody oran antibody derivative or an antibody fragment capable of binding toLgr5 or 6, i.e. an antibody or derivative or fragment thereof that hasaffinity for Lgr5 or 6. As Lgr5 and 6 are transmembrane surfaceproteins, such an antibody or a derivative or a fragment thereofpreferably has affinity for the part of the protein facing externally,i.e. binds to any extracellular part of said protein.

In a preferred embodiment, said antibody or an antibody derivative or anantibody fragment has a high affinity for Lgr5 and/or 6, i.e. anaffinity with a Kd of at least 10⁻⁷. Preferably the affinity is ≤10⁻⁹.However, affinities of around 10⁻⁸ can also be used.

Hence, in a preferred embodiment, the invention provides a method forobtaining (or isolating) cancer stem cells comprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound,

wherein said Lgr5 or 6 binding compound is an antibody or an antibodyderivative or an antibody fragment capable of binding to Lgr5 or 6.

Antibodies or their derivatives or their fragments can be provided bymethods that are well known to the person skilled in the art and includethe hybridoma technique, single chain-antibody/phage display technology.

As non-limiting examples, the experimental part describes Lgr5-specificand Lgr6-specific antibodies. A method according to the invention,wherein an antibody as depicted in Table 4 or 5 is used is thereforealso herewith provided, as well as a method according to the invention,wherein an antibody or an antibody derivative or an antibody fragment isused which comprises at least one CDR sequence as depicted in FIG. 27.Preferably, said antibody or antibody derivative or antibody fragmentcomprises a CDR1 sequence and a CDR2 sequence and a CDR3 sequence of alight chain and/or heavy chain depicted in FIG. 27.

Examples of suitable antibody fragments are scFv, Fab. Examples ofsuitable derivatives are chimeric antibodies, nanobodies, bifunctionalantibodies or humanized antibodies. In yet another preferred embodiment,the used antibody is a monoclonal antibody.

Another example of an Lgr5 or 6 binding compound is an Lgr5 or 6 ligandwhich can be used unmodified, but can also be produced and/or used as afusion protein or can be coupled to a second moiety to allow cellseparation.

In a preferred embodiment, the invention therefore provides a method forobtaining (or isolating) cancer stem cells comprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound,

wherein said Lgr5 or 6 binding compound is an Lgr5 or 6 ligand.

The person skilled in the art is very well capable of producing an Lgr5or 6 ligand fusion protein, for example via standard molecular biologytechniques.

A suitable example of an Lgr5 or 6 ligand is a member of the insulinpeptide family, such as Ins15 or relaxin3. Another suitable example is acysteine-knot protein such as Noggin, Gremlin, Dan, or Cerberus. Basedon the known and published nucleotide and amino acid sequences of theseligands, the preparation of a fusion protein is well within theabilities of the person skilled in the art.

Preferably the second moiety introduces a feature which allows for easyidentification and tracing of the fusion protein, for example a protein(fragment) such as the antibody Fc tail or Staphylococcal protein A orGlutathion-S-transferase, a short antigenic peptide tag such as the Myc,FLAG or HA tag or an oligomeric Histidine-tag, an enzymatic tag such asAlkaline Phosphatase, a fluorescent protein tag (such as GreenFluorescent Protein). Small chemical moieties can also be coupled to theligand for cancer stem cell identification and/or isolation. Thesemoieties can be recognized and bound by specific antibodies, or can havespecific affinity for a material to be used in cell separation, or canfor instance be fluorescent, radioactive or magnetic properties. In aneven more preferred embodiment, the second part of the fusion protein islinked to said Lgr5 or 6 ligand via a spacer. Even more preferable, saidspacer comprises an enzyme digestible sequence. This allows for an easyseparation of the second moiety and the Lgr5 or 6 ligand.

Yet another example of an Lgr5 or 6 binding compound is a small compoundthat has affinity for Lgr5 or 6.

In a preferred embodiment, the invention thus provide a method forobtaining (or isolating) cancer stem cells comprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound,

wherein said Lgr5 and/or 6 binding compound a small molecule withaffinity for Lgr5 and/or 6. Such a small molecule is for example asynthetic peptide or a small chemical compound.

In a preferred embodiment, the affinity of said small molecule for Lgr5or 6 is a high, i.e. an affinity with a Kd of at least 10⁻⁷.

Such a small molecule is optionally coupled to a second moiety thatintroduces a feature which allows for easy identification and tracing ofthe fusion protein, for example a protein (fragment) such as theantibody Fc tail or Staphylococcal protein A orGlutathion-S-transferase, a short antigenic peptide tag such as the Myc,FLAG or HA tag or an oligomeric Histidine-tag, an enzymatic tag such asAlkaline Phosphatase, a fluorescent protein tag such as GreenFluorescent Protein).

Depending on the desired cancer stem cell and the now known presence orabsence of Lgr5 or 6, a method according to the invention can use atleast one, at least two, at least three or even more (different) bindingcompound(s). Table 3 provides an overview of the presence of absence ofLgr5 or 6 on the different kind of tumors. Based on this Table theperson skilled in the art is very well capable of selecting one ormultiple target markers and one or multiple corresponding bindingcompounds and thus capable of obtaining or isolating cancer stem cells.

TABLE 3 The distribution of the stem cell markers Lgr5 and 6 in tumors.Data is derived from comparison of Lgr5 or Lgr6 expression in normalversus tumor tissues by microarray analysis (Genelogic) or byquantitative PCR. Cancer stem Marker cell Lgr5 Lgr6 brain + + kidney − −liver + − lung − + retina + − stomach + − Colon/rectal + + head andneck + + testis + + breast + + hair follicle + + prostate + + ovary + +skin + + leukemia + − chondrosarcoma + + muscle/soft + − tissueuterus + + retinoblastoma − +

If the person skilled in the art wants to obtain breast cancer stemcells, a binding compound of Lgr5 or 6 can be used alone or in anycombination thereof, because the breast cancer stem cells comprise bothof said markers.

In a preferred embodiment, the invention provides a method for obtaining(or isolating) cancer stem cells comprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound,

wherein

-   -   said Lgr5 or 6 binding compound is an Lgr5 binding compound and        wherein said cancer stem cells are brain, liver, retina,        stomach, colon, head and/or neck, testis, prostate, ovary, skin,        hair follicle, leukemia, chondrosarcoma, muscle/soft tissue,        uterus, or breast stem cells; or    -   said Lgr5 or 6 binding compound is an Lgr6 binding compound and        wherein said cancer stem cells are brain, lung, head and/or        neck, testis, breast, hair follicle, skin, prostate,        chondrosarcoma, uterus, retinoblastoma, or ovary stem cells; or    -   said Lgr5 or 6 binding compound is at least one Lgr6 binding        compound in combination with at least one Lgr5 binding compound        and wherein said cancer stem cells are brain, skin, head and/or        neck, testis, breast, prostate, ovary, chondrosarcoma, uterus,        or hair follicle stem cells.

In a preferred embodiment, the invention provides a method for obtaining(or isolating) cancer stem cells comprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound,

wherein one binding compound is used.

In yet another preferred embodiment, the invention provides a method forobtaining (or isolating) cancer stem cells comprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound,

wherein at least two different binding compounds are contacted with saidcell suspension. Said two different binding compounds can be directedagainst one and the same marker (for example directed to Lgr5). Forexample, use can be made of two antibodies directed to two differentepitopes which antibodies together provide (a preferably essentiallycomplete) capture of the desired stem cells. However, said two differentbinding compounds can also be directed to two different stem cellmarkers (for example to Lgr6 and Lgr5). Whenever use is made of two orthree or even more binding compounds, said binding compounds may be fromthe same class of binding compounds (for example all being antibodies,small molecules or ligand (fusion proteins)) or may be from differentclasses of binding compounds (for example an antibody directed to Lgr6and a ligand fusion protein for binding to Lgr5).

In a preferred embodiment, at least two different antibodies or antibodyderivatives or antibody fragments capable of binding to Lgr5 and/or 6are contacted with a cell suspension.

After allowing the binding compounds to interact with the cellsuspension (for a certain amount of time or under different conditionssuch as pH, temperature, salt etc.), subsequent identification ofobtained bound complexes is performed. This is for example accomplishedby using FACS analysis. Fluorescence-activated cell-sorting (FACS) is aspecialised type of flow cytometry. It provides a method for sorting aheterogenous mixture of biological cells into two or more containers,one cell at a time, based upon the specific light scattering andfluorescent characteristics of each cell. It is a useful scientificinstrument as it provides fast, objective and quantitative recording offluorescent signals from individual cells as well as physical separationof cells of particular interest.

In a preferred embodiment, the invention provides a method for obtaining(or isolating) cancer stem cells, or a collection of cancer stem cells,comprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound,

wherein a FACS is used to identify and sort the cells that bind to anLgr5 and/or 6 binding compound, and wherein said collection comprises atleast 50% of cancer stem cells that are able to recapitulate thegeneration of a continuously growing tumor. Preferably, said collectioncomprises at least 60%, more preferably at least 70%, more preferably atleast 80%, more preferably at least 90%, more preferably at least 95% ofcancer stem cells that are able to recapitulate the generation of acontinuously growing tumor.

Other options for identification of bound complexes are magnetic beadsorting, (immuno)affinity column cell separation, or (immuno)affinitypanning.

For analysis by FACS, the binding compound is preferably provided with afluorescence label, for analysis by magnetic bead sorting the bindingcompound is preferably provided with magnetic beads (for example anantibody-coated magnetic bead).

In yet another embodiment, the invention provides (a collection of)cancer stem cells comprising Lgr5 and/or 6 embedded in their cellmembrane, wherein said collection comprises at least 50% of cancer stemcells that are able to recapitulate the generation of a continuouslygrowing tumor. In a preferred embodiment said collection comprises atleast 60% pure cancer stem cells, preferably at least 70% pure cancerstem cells, more preferably at least 80% pure cancer stem cells, morepreferably at least 90% pure cancer stem cells, more preferably at least95% pure cancer stem cells. More preferably said collection consists of(cancer) stem cells with the indicated purity. Such a collection ofcancer stem cells is for example obtained by a method as describedherein, i.e. a method for obtaining (or isolating) cancer stem cellscomprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound.

Examples of cancer stem cells that can be obtained via the abovementioned methods are colon, rectal, intestine, skin, retina, brain,breast, testis, hair follicle, stomach, head and/or neck, liver, lung,prostate, esophagus, adrenal medulla, heart, or ovarian cancer stemcells.

If necessary, said cancer stem cells are maintained or multiplied(expanded) by culturing said cells in the presence of an Lgr5 and/or 6ligand under appropriate environmental conditions (for example pH andtemperature). A suitable example of an Lgr5 or 6 ligand is a member ofthe insulin peptide family, such as Ins15 or relaxin3. Another suitableexample is a cysteine-knot protein such as Noggin, Gremlin, Dan, orCerberus.

Hence, in yet another embodiment, the invention provides a method formaintaining or culturing cancer stem cells, comprising providing cancerstem cells with an Lgr5 and/or 6 ligand or a small binding molecule ofLgr5 or 6.

The invention further provides a collection of (isolated) cancer stemcells of the invention further comprising an Lgr5 and/or Lgr6 bindingcompound associated with Lgr5 and/or Lgr6 expressed by said cancer stemcells. The invention further provides a culture of (isolated) cancerstem cells comprising an Lgr5 and/or Lgr6 binding compound. Preferablysaid Lgr5 and/or Lgr6 binding compound is a specific Lgr5 and/or Lgr6binding antibody or a fragment or derivative thereof.

In a preferred embodiment, the invention provides a recombinant tumorstem cell, isolated according to a method of the invention, comprising areporter gene under control of a Lgr5 or Lgr6 promoter such that thereporter gene product is expressed in cells expressing Lgr5 or Lgr6. Areporter gene construct, in which the reporter gene is operably linkedto a Lgr5 or Lgr6 promoter, can be inserted into the genome of anisolated tumor stem cell. Alternatively, said reporter gene constructcan be provided, for example, through infection of a tumor stem cellwith an adenoviral vector comprising the reporter gene construct.Methods for inserting a reporter gene construct into the genome of acell are known to a skilled person and include random insertion, forexample by insertion of a retrovirus comprising the reporter geneconstruct, or through homologous recombination.

In a further preferred embodiment, the invention provides a recombinantstem cell comprising a first reporter gene under control of a Lgr5 orLgr6 promoter such that the reporter gene product is expressed in cellsexpressing Lgr5 or Lgr6, a sequence encoding a regulatable protein beingin an operable linkage with the first reporter gene such that theregulatable protein is co-expressed with the first reporter gene productin cells expressing Lgr5 or Lgr6, and a second reporter gene that isexpressed upon activation of the regulatable protein.

Said first reporter gene product preferably is a fluorescent proteinsuch as green fluorescent protein, or more preferred enhanced greenfluorescent protein. Said regulatable protein preferably is CRE-ERT2.The second reporter gene preferably comprises LacZ.

Isolated (and optionally cultured) cancer stem cells are for exampleuseful for the further analysis of such cells on for examplebiochemical, molecular biology or marker level.

Moreover, isolated cancer stem cells are also very useful in theidentification of compounds that can be used in cancer treatment,especially cancer stem cell therapy. Based on the knowledge that Lgr5and/or 6 are embedded in the cell membrane of cancer stem cells,compounds capable of inhibiting, blocking or binding to Lgr5 and/or 6can be designed and prepared. Such compounds can subsequently be testedfor their ability to kill or functionally block or inhibit cancer stemcells comprising Lgr5 and/or 6 in their cell membrane.

Recombinant tumor stem cells according to the invention are particularlypreferred for the identification of compounds, because their presencecan readily be monitored after addition of a compound. Said recombinanttumor stem cells are suited for use in assays such a high throughputassays, where multiple compounds are tested in a cost-efficient manner.

In another embodiment, the invention thus provides a method for testingthe effect of a possible anti cancer stem cell compound comprisingcontacting (treating) a set of cancer stem cells according to theinvention in vitro with said possible anti cancer stem cell compound andtesting whether said treated cancer stem cells are capable of generatinga continuously growing tumor and wherein said possible cancer stem cellcompound is preferably designed as an Lgr5 or 6 inhibitor or as an Lgr5or 6 binding compound.

In yet another embodiment, the invention provides a method for testingthe effect of a possible anti cancer stem cell compound comprisingcontacting a collection of cancer stem cells according to the inventionin vitro with said possible anti cancer stem cell compound and testingwhether said treated cancer stem cells are capable of generating acontinuously growing tumor, further comprising contacting said possibleanti cancer stem cell compound with a tissue of organ stem cell andselecting a compound that specifically effects tumour stem cells.

The cancer stem cells used in this method comprise Lgr5 and/or 6 intheir cell membrane or are obtainable by a method for obtaining (orisolating) cancer stem cells comprising

optionally preparing a cell suspension from a solid or liquid tumorsample

contacting said cell suspension with an Lgr5 and/or 6 binding compound

identify or obtaining the cells bound to said binding compound

optionally isolating the cancer stem cells from said binding compound.

The to be tested compounds can for example be obtained from a (small)compound library or can be specifically designed based on the(structural) knowledge of Lgr5 or 6 or on the (structural) knowledge ofa (natural) ligand of Lgr5 or 6.

The anti cancer stem cell compounds will be discussed in more detailbelow.

In yet a further embodiment, the invention provides an Lgr5 or 6inhibitor or an Lgr5 or 6 binding compound. Preferably such an inhibitoror binding compound is obtainable by a method for testing the effect ofa possible anti cancer stem cell compound comprising contacting(treating) a set of cancer stem cells according to the invention invitro with said possible anti cancer stem cell compound and testingwhether said treated cancer stem cells are capable of generating acontinuously growing tumor and wherein said possible cancer stem cellcompound is preferably, but nor necessarily, designed as an Lgr5 or 6inhibitor or as an Lgr5 or 6 binding compound.

A first example of an Lgr5 or 6 inhibitor is an inhibitor of Lgr5 or 6protein. Preferably said Lgr5 or 6 protein inhibitor is an antibody orantibody derivative or antibody fragment capable of binding to Lgr5 or 6and more preferably capable of binding to the part of Lgr5 or 6 that isexposed on the outside of the cancer stem cell. In yet another preferredembodiment, said antibody or antibody derivative or antibody fragmentbinds to said Lgr5 or 6 protein and functionally blocks said Lgr5 or 6protein by preventing the binding of a natural ligand of Lgr5 or 6. Inone embodiment, said antibody or antibody derivative or antibodyfragment comprises at least one CDR sequence as depicted in FIG. 27.Preferably, said antibody or antibody derivative or antibody fragmentcomprises a CDR1 sequence and a CDR2 sequence and a CDR3 sequence of alight chain and/or a heavy chain depicted in FIG. 27. In a furtherembodiment, said antibody is an antibody as depicted in Table 4 or 5.

Examples of suitable antibody fragments are scFv and Fab. Examples ofsuitable derivatives are chimeric antibodies, nanobodies, bifunctionalantibodies or humanized antibodies.

In yet another preferred embodiment, the used antibody is a monoclonalantibody.

Another example of an Lgr5 or 6 protein inhibitor is a small moleculethat interferes with the biological activity of Lgr5 or 6. Such a smallmolecule can be a chemical compound as well as a small protein and istypically designed on the basis of structure-function analysis of Lgr5or 6. Analysis can comprise crystal structure analysis of Lgr5 or 6.Small molecules libraries can be screened or compounds can be designedand subsequently screened. A small molecule inhibitor can also bedesigned based on the structure of a (natural) ligand of Lgr5 or 6.

Yet another example of an Lgr5 or 6 inhibitor is an inhibitor of themRNA transcripts of Lgr 5 or 6. One example of an inhibitor of Lgr5 or 6transcript are antisense molecules. Antisense drugs are complementarystrands of small segments of mRNA. Such an antisense molecule binds tothe mRNA of Lgr5 or 6 and inhibits (at least in part) Lgr5 or 6 proteinproduction. Another example of an inhibitor of Lgr5 or 6 transcriptrelate to RNA interference (RNAi) molecules such as siRNA molecules.

Besides the option that an antibody or antibody derivative or antibodyfragment binds to Lgr5 or 6 and functionally blocks Lgr5 or 6 (asdescribed above), said antibody or antibody derivative or antibodyfragment can also bind to Lgr5 or 6 without functionally blocking theLgr5 or 6 activity. Such an antibody or antibody derivative or antibodyfragment is preferably coupled to another compound (i.e. another moiety)that is capable of functionally inhibiting a cancer stem cell. Anexample of such another compound is a toxin. Hence, the invention alsoprovides a cancer stem cell inhibitor, wherein said inhibitor comprisesa first part that is capable of binding to Lgr5 or 6 and a second partthat provides for cancer stem cell dysfunction. Preferably, said firstpart is an antibody or antibody derivative or antibody fragment binds toLgr5 or 6 (preferably without influencing the function of Lgr5 or 6) andsaid second part is a toxin. In this embodiment Lg5 or 6 is used as atarget to deliver a cytotoxic compound to a cancer stem cell.

Thus, the invention also provides a binding compound according to theinvention that is linked to a toxic agent or linked to an enzyme capableof converting a prodrug to a toxic agent. For example, the antibody orderivative or fragment thereof is linked to a toxic agent to form animmunoconjugate. Said toxic agent includes a radioisotope and a toxicdrug which is ineffective when administered systemically alone. Bycombining the targeting-specificity of a binding compound of theinvention to Lgr 5 and/or 6-expressing tumor stem cells with the killingpower of a toxic effector molecule, immunoconjugates permit sensitivediscrimination between target and normal tissue, resulting in fewertoxic side effects than most conventional chemotherapeutic drugs.Examples of prodrugs that can be targeted to Lgr 5 or 6-expressing tumorstem cells comprise benzoic acid mustard whereby the antibody isconjugated to carboxypeptidase G2; nitrogenmustardcephalosporin-p-phenylenediamine whereby the antibody isconjugated to beta-lactamase; andcyanophenylmethylbeta-D-gluco-pyranosiduronic acid, whereby the antibodyis conjugated to beta-glucosidase.

The invention further provides a use of a binding compound according tothe invention as a medicament for treatment of cancer. In a preferredembodiment said binding compound comprises an antibody specific for Lgr5and/or Lgr6 or an Lgr5 or 6 binding fragment or derivative thereof. In apreferred embodiment said antibody is a human, humanized or deimmunisedanti Lgr5 and/or Lgr6 antibody as described herein. In a preferredembodiment said binding compound is specific for human Lgr5 and/or humanLgr6. Preferably said antibody is a monoclonal antibody. In oneembodiment, said binding compound is an antibody or antibody derivativeor antibody fragment which comprises at least one CDR sequence asdepicted in FIG. 27. Preferably, said antibody or antibody derivative orantibody fragment comprises a CDR1 sequence and a CDR2 sequence and aCDR3 sequence of a light chain and/or a heavy chain depicted in FIG. 27.In a further embodiment, said binding compound is an antibody asdepicted in Table 4 or 5. In a preferred embodiment, a binding compoundaccording to the invention is linked to a toxic agent or linked to anenzyme capable of converting a prodrug to a toxic agent.

In yet another embodiment, the invention provides a cancer stem cellinhibitor comprising an Lgr5 or 6 ligand preferably coupled to anothercompound (i.e. another moiety) that is capable of functionallyinhibiting a cancer stem cell. An example of such another compound is atoxin. Examples of an Lgr5 or 6 ligand are ligands that are a member ofthe insulin peptide family. Suitable examples are Ins15 and relaxin3.Another suitable example is a cysteine-knot protein such as Noggin,Gremlin, Dan, or Cerberus. Moreover, a natural ligand can be modifiedsuch that it permanently blocks Lgr5 or 6 activity.

All the above mentioned Lgr5 or 6 protein inhibitors, inhibitors of themRNA transcripts of Lgr5 or 6, as well as the described cancer stem cellinhibitors are very useful for therapeutic cancer therapy approaches.

In yet another embodiment, the invention provides the use of at leastone Lgr5 or 6 inhibitor or at least one Lgr5 or 6 binding compound asdescribed herein (e.g. an Lgr5 or 6 protein inhibitor or an inhibitor ofthe mRNA transcripts of Lgr5 or 6 or a cancer stem cell inhibitor) forthe manufacture of a medicament for the treatment of cancer.

Preferably, said inhibitors are obtainable according to a method of theinvention, i.e. a method for testing the effect of a possible anticancer stem cell compound comprising contacting (treating) a set ofcancer stem cells according to the invention in vitro with said possibleanti cancer stem cell compound and testing whether said treated cancerstem cells are capable of generating a continuously growing tumor andwherein said possible cancer stem cell compound is preferably designedas an Lgr5 or 6 inhibitor or as an Lgr5 or 6 binding compound. In apreferred embodiment, use is made of an Lgr5 or 6 inhibitor or an Lgr5or 6 binding compound.

The invention further provides a method for reducing or inhibiting tumormaintenance potential of a tumor, comprising providing said tumor with acompound that is designed as an Lgr5 and/or 6 inhibitor, or preferablythat is capable of binding to Lgr5 and/or 6.

An anti cancer stem cell therapy is very useful to eradicate the part ofthe tumor that maintains the tumor and is involved in invasive growthand metastasis. Although such an approach is considered to be a veryeffective cancer therapy, improved or increased results can be obtainedby combining the anti cancer stem cell therapy with conventional cancertherapy.

In a preferred embodiment, the invention provides the use of at leastone Lgr5 or 6 inhibitor or at least one Lgr5 or 6 binding compound asdescribed herein (e.g. an Lgr5 or 6 protein inhibitor or an inhibitor ofthe mRNA transcripts of Lgr5 or 6 or a cancer stem cell inhibitor) forthe manufacture of a medicament for the treatment of cancer, furthercomprising general anti-cancer therapy. Examples of said general (orconventional) anti-cancer therapy are radiation, chemotherapy,antibody-based therapy or small molecule based treatments. Combinedtreatment leads to an approach of killing the minority cancer stem cellpopulation as well as the bulk of the tumor.

In another preferred embodiment, the invention provides the use of atleast one Lgr5 or 6 inhibitor or at least one Lgr5 or 6 binding compoundas described herein (e.g. an Lgr5 or 6 protein inhibitor or an inhibitorof the mRNA transcripts of Lgr5 or 6 or a cancer stem cell inhibitor)for the manufacture of a medicament for the treatment of cancer, whereincancer stem cells are involved in intestinal cancer, colon cancer,rectal cancer, colorectal cancer, skin cancer, esophageal cancer, breastcancer, prostate cancer, medulloblastoma or other brain cancers, livercancer, stomach cancer, hair follicle cancer, retinal cancer,pheochromcytoma, head and neck cancer, testicular cancer, ovariancancer, basel cell carcinoma of the skin or lung cancer. In thisrespect, “involved” means sustaining and/or maintaining and/orexpanding.

Preferably, the treatment with at least one Lgr5 and/or 6 inhibitor orat least one Lgr5 and/or 6 binding compound is initiated before, afteror during said conventional cancer therapy.

Although treatment with at least one Lgr5 and/or 6 inhibitor or at leastone Lgr5 and/or 6 binding compound is considered to be effective,treatment with multiple inhibitors and/or binding compounds can provideimproved results. This is especially true if the to be treated cancerstem cell comprises two, three or even more different Lgr proteinsembedded in its cell membrane.

In a preferred embodiment, the invention provides the use of at leastone Lgr5 and/or 6 inhibitor or at least one Lgr5 and/or 6 bindingcompound as described herein (e.g. an Lgr5 or 6 protein inhibitor or aninhibitor of the mRNA transcripts of Lgr5 or 6 or a cancer stem cellinhibitor) for the manufacture of a medicament for the treatment ofcancer, wherein at least two Lg5 and/or 6 inhibitors or at least twoLgr5 and/or 6 binding compounds or a combination of at least one Lgr5and/or 6 inhibitor and at least one Lgr5 and/or 6 binding compoundare/is used.

The invention thus provides use of at least two Lgr5 and/or 6 inhibitorsor at least two Lgr5 and/or 6 binding compounds or a combination of atleast one Lgr5 and/or 6 inhibitor and at least one Lgr5 and/or 6 bindingcompound for the manufacture of a medicament for the treatment of cancerstem cells. An inhibitor and/or binding compound can, but need not be,directed to one and the same Lgr protein, e.g. a binding compound and aninhibitor against Lgr5. The mixture of at least two Lgr5 or 6 inhibitorsor at least two Lgr5 or 6 binding compounds or a combination of at leastone Lgr5 or 6 inhibitor and at least one Lgr5 or 6 binding compound isfor example directed against Lgr5 and 6. The latter is especially usefulin a method for obtaining brain, head and neck, testis, breast,prostate, skin, ovary or hair follicle cancer stem cells.

Another already described useful compound is a stem cell inhibitorcomprising an Lgr5 and/or 6 ligand preferably coupled to anothercompound (i.e. another moiety) that is capable of functionallyinhibiting a cancer stem cell. An example of such another compound is atoxin. Examples of an Lgr5 or 6 ligand are ligands that are a member ofthe insulin peptide family. Suitable examples are Ins15 and relaxin3.Another suitable example is a cysteine-knot protein such as Noggin,Gremlin, Dan, or Cerberus. Such a compound can also be used in a cancerstem cell therapy.

Therefore, the invention provides use of a compound that is capable ofbinding to a ligand of Lgr5 and/or 6 for the manufacture of a medicamentfor the treatment of cancer stem cells. Preferably, said ligand iscoupled to another compound (i.e. another moiety) that is capable offunctionally inhibiting a cancer stem cell, such as a toxin or an enzymecapable of converting a prodrug to a toxic agent. Even more preferably,such a treatment is combined with general cancer therapy, such asradiation, chemotherapy, antibody-based therapy or small molecule basedtreatments.

In yet another embodiment, the invention provides use of a compound thatis capable of binding to a ligand of Lgr5 and/or 6 for the manufactureof a medicament for the treatment of cancer stem cells. Preferably thebinding of said compound to an Lgr5 and/or 6 ligand is such that saidligand is no longer capable of binding to Lgr5 and/or 6. An example isan antibody or antibody derivative or antibody fragment that captures a(natural) ligand of Lgr5 and/or 6 and thus prevents the activation ofLgr5 and/or 6.

The invention further provides a composition comprising at least oneLgr5 and/or 6 inhibitor or at least one Lgr5 and/or 6 binding compoundor at least one Lgr5 and/or 6 ligand or at least one compound capable ofbinding to an Lgr5 and/or 6 ligand, preferably all as described hereinbefore. Preferably said composition is a pharmaceutical composition.Such a pharmaceutical composition can further comprise anypharmaceutically acceptable excipient, stabilizer, activator, carrier,permeator, propellant, desinfectant, diluent and/or preservative. Apharmaceutical composition may be in any desired form, e.g. a tablet,infusion fluid, capsule, syrup, etc.

In a further preferred embodiment a (pharmaceutical) compositioncomprises at least two Lgr5 and/or 6 inhibitors or at least two Lgr5and/or 6 binding compounds or a combination of at least one Lgr5 and/or6 inhibitor and at least one Lgr5 and/or 6 binding compound.

Now that the inventors have disclosed that Lgr5 and/or 6 are cancer stemcell markers this further opens possibilities in the field ofdiagnostics. One can for example use an Lgr5 and/or 6 binding compoundto determine the cancer stem cell content of a tumor or to determine thepresence or absence of a cancer stem cell in a body fluid such as blood.Preferably, the binding compound has a high affinity for Lgr5 or 6 (i.e.the Kd is at least 10⁻⁷). Suitable binding compounds are an Lgr5 and/or6 ligand, an antibody or an antibody derivative or an antibody fragmentcapable of binding to Lgr5 and/or 6, e.g. an antibody or derivative orfragment thereof that has affinity for Lgr5 and/or 6.

The invention thus also provides a method for determining cancer stemcell content of a tumor, comprising contacting said tumor with an Lgr5and/or 6 binding compound, removing unbound binding compound anddetermining whether any bound binding compound is present in said tumor.

In a preferred embodiment, said method is an in vitro method. Even morepreferably, said binding compound is labeled such that it can beidentified. Suitable labels are for example a protein (fragment) such asthe antibody Fc tail or Staphylococcal protein A orGlutathion-S-transferase, a short antigenic peptide tag such as the Myc,FLAG or HA tag or an oligomeric Histidine-tag, an enzymatic tag such asAlkaline Phosphatase, a fluorescent protein tag (such as GreenFluorescent Protein). However, it is also possible to use a secondcompound that has affinity for the binding compound and labeling saidsecond compound with a suitable label (i.e. an indirect analysis).

For in vivo application, the invention further provide use of an Lgr5and/or 6 binding compound in the preparation of a diagnostic for thediagnosis of cancer stem cell presence and/or content in a tumor.

Said sample is for example obtained from a body fluid or a sampleobtained from a solid tumor.

In a preferred embodiment, the invention provides a method fordetermining cancer stem cell content of a tumor, comprising contactingsaid tumor with an Lgr5 and/or 6 binding compound and determiningwhether any bound binding compound is present in said tumor. Theinvention also provides use of an Lgr5 and/or 6 binding compound in thepreparation of a diagnostic for the diagnosis of cancer stem cellpresence and/or content in a sample, wherein said binding compound isconjugated to a substance that allows radioactive imaging, positronemission tomography (PET) scanning, magnetic resonance imaging (MRI)scanning, or X-ray/computed tomography (CT) scanning.

The invention further provides a method for determining whether a bodyfluid comprises a cancer stem cell, comprising

optionally obtaining a sample from said body fluid

contacting said body fluid with an Lgr5 and/or 6 binding compound

removing unbound binding compound

detecting any bound complex comprising an Lgr5 and/or 6 bindingcompound, and determining the presence of a cancer stem cell based onthe presence of detected bound complex.

Suitable binding compounds are an Lgr5 and/or 6 ligand, an antibody oran antibody derivative or an antibody fragment capable of binding toLgr5 and/or 6, i.e. an antibody or derivative or fragment thereof thathas affinity for Lgr5 and/or 6.

The step of removing any unbound binding compound is for exampleaccomplished by washing with a suitable solution or buffer.

Examples of body fluid are blood, urine, lymph fluid or tears.

In a preferred embodiment, said method is an in vitro method.

Suitable labels have been mentioned above.

The described diagnostic methods are also very useful for determiningwhether an anti cancer therapy leads to eradication of (at least part ofthe) cancer stem cells. If for example use is made of general anticancer therapy (or combined treatment with for example an Lgr5 and/or 6inhibitor), the effect of said therapy on the cancer stem cell can bedetermined by determining the presence or absence of cells bearing Lgr5and/or 6.

In yet another embodiment, the invention provides a method fordetermining the effectivity of an anti cancer treatment, comprisingtreating cancer and determining whether cancer stem cells are presentcomprising contacting said cancer with an Lgr5 and/or 6 bindingcompound.

Such a method can be performed in vitro as well as in vivo.

Preferably the presence of cancer stem cells is determined beforetreatment and during or after treatment such that it can determinedwhether or not the applied treatment results in a changed (preferablydecreased) amount of cancer stem cells.

The invention further provides a method for treating an individual inneed thereof comprising administering an effective amount of a hereindescribed pharmaceutical composition to said individual and optionallyfurther subjecting said individual to conventional cancer therapy suchas radiation or chemotherapy.

The invention will be explained in more detail in the following,non-limiting examples.

FIGURE LEGENDS

FIG. 1. Gpr49/Lgr5 is a Wnt target gene in a human colon cancer cellline and is expressed in mouse crypts. a: Northern blot analysis (upperpanel); ethidium bromide-stained gel (lower panel). Lane 1: ControlLs174T-L8 cells. Lane 2: Ls174T cells after 24 hours doxycycline inducedWnt pathway inhibition as in 6 (References 2). Note the strongdownregulation of the 4.4 kb Grp49 mRNA upon Wnt pathway inhibition.Lane 3: RNA extracted from isolated mouse small intestinal crypts, whichunavoidably suffers from limited degradation resulting in some smearing.Lane 4: RNA extracted from isolated mouse villi. Note the specificexpression of Grp49 in mouse crypts. b/c Two overlapping images of anin-situ hybridization performed on small intestines of an APCmin mouse,illustrating the ubiquitous expression of Grp49 at crypt bottoms(examples marked with white arrows) and the expression in the adenoma inthe left panel (marked by a broken line).

FIG. 2. Gpr49/Lgr5 expression in cycling Crypt Base Columnar (CBC) cellsof the small intestine. a-c, In-Situ hybridization was performed withprobes specific for 3 Tcf target genes demonstrating non-overlappingexpression patterns on the crypt epithelium. a: Cryptdin specificallymarks Paneth cells at the crypt base; b: KIAA0007 marks the TA cellslocated above the Paneth cells c: Gpr49/Lgr5 is specifically expressedin 4-8 cells intermingled with the Paneth cells at the crypt base. Allsense controls were negative (not shown). d: CBC cells (circled) areonly poorly visible on heamatoxylin/eosin stained sections. e: CBC cells(circled) are KI67+f: Some CBC cells express the M-phase markerphospho-histidine H3 (circled). g: BrdU incorporation in CBC cells 4hours after a single dose of BrdU (circled). h: BrdU incorporation inCBC cells after 24 hour continuous BrdU labeling (circled). Black bars:Numbers of BrdU-positive CBC cells per crypt section after 4 hours or 24hours. White bar: Total number of CBC cells per crypt section assessedby counting LacZ-positive cells in Gpr49-LacZ mice.

FIG. 3. Restricted expression of a GPR49-LacZ reporter gene in adultmice a: Generation of mice carrying lacZ integrated into the last exonof the Gpr49 gene, removing all transmembrane regions of the encodedGpr49 protein. b-h, Expression of GPR49lacZ in selected adult mousetissues. b/c: In the small intestine expression is restricted to 6-8slender cells intermingled with the Paneth cells at the crypt base. d/e:In the colon, expression is confined to a few cells located at the cryptbase. f/g: Expression in the stomach is limited to the base of theglands. h: In the mammary glands, expression was evident only insmaller, actively proliferating glands, where it was restricted to basalepithelial cells. i: In the skin, expression occurs in the outer rootsheath of the hair follicles in a domain extending from the bulge to thedermal papilla.

FIG. 4. EGFP expression in a GPR49-EGFP-Ires-CreERT2 knock-in mousefaithfully reproduces the GPR491acZ expression pattern in the intestinaltract. a: Generation of mice expressing EGFP and CreERT2 from a singlebicistronic message by gene knock-in into the first exon of Gpr49.b,c,e: Confocal GFP imaging counterstained with the red DNA dye ToPro-3confirms that Gpr49 expression is restricted to the 6-8 slender cellssandwiched between the Paneth cells at the crypt base of the smallintestine. b: Entire crypt-villus unit; c: enlargement of crypt regions;d: Immunohistochemical analysis of EGFP expression in intestinal crypts.e: 2D image of 3D reconstruction supplied as supplemental movie in FIG.7. Confocal imaging of EGFP expression in the colon confirms Gpr49expression is restricted to a few cells located at the crypt base. g:CryoEM section of crypt stained for GFP with immunogold (scale bar=1000nm). Quantification of specificity of labeling: Gold particles werecounted over 255 μm2 of CBC cell cytosol (1113 particles), 261 μm2 ofPaneth cell cytosol (305 particles) and 257 μm2 of fibroblast cytosol(263 particles) outside the crypt. Thus CBC cytoplasm had 4.36 goldparticles/μm2 compared to the Paneth cells 1.17 gold particles/μm2 andto the fibroblast control 1.02 gold particles/μm2. C=Crypt lumen;P=Paneth cells; CBC=Crypt Base Columnar cells. h: Unlabeled CryoEMsection (scale bar=2000 nm), underscoring the ultrastructuralcharacteristics of CBC cells and their positioning relative to Panethcells.

FIG. 5. Lineage tracing in the small intestine and colon. a:GPR49-EGFP-Ires-CreERT2 knock-in mouse crossed with Rosa26-LacZ reportermice 12 hours after Tamoxifen injection b: frequency at which the bluecells appeared at specific positions relative to the crypt bottom,according to the scheme in the inset of FIG. 5b . The large majority ofthe Cre+ LacZ-labeled CBC cells occurred at positions between the Panethcells, while only 10% of these cells were observed at the +4 positiondirectly above the cells (blue line). Quantitative data on the positionof long term DNA label-retaining cells obtained in adult micepost-irradiation (marking the “+4” intestinal stem cell) were publishedrecently by Potten and colleagues17. Comparison of these data (red line)with the position of CBC cells carrying activated Cre. c-e: Histologicalanalysis of LacZ activity in small intestine 1 day post-induction (c), 5days post-induction (d) and 60 days post-induction (e). f-h:Double-labelling of LacZ-stained intestine using PAS demonstrates thepresence of Goblet cells (f; white arrows) and Paneth Cells (g; bluearrows) in induced blue clones. Double-labelling with Synaptophysindemonstrates the presence of enteroendocrine cells within the inducedblue clones (h; black arrows). i-k Histological analysis of LacZactivity in colon 1 day post-induction (1), 5 days post-induction (j)and 60 days post-induction (k).

FIG. 6. Strategy for EGFP-ires-CreERT2 cassette knock-in into the Gpr49locus

a: Schematic structure of the mouse Gpr49 gene

b: Southern blotting strategy to screen ES cells transfected with aknock-in construct targeting the ATG translational start in Exon I.

c: Four ES cell clones out of a total of 500 scored positive for therecombined BamHI band running at 4.3 kb. After re-screening of these 4ES clones, the first two (asterisks) were selected for blastocystinjections.

FIG. 7. Relative radiation sensitivity of CBC cells, +4 cells, and TAcells. Adult mice were irradiated with 1 Gy or 10 Gy and subsequentlysacrificed 6 hours later, at the peak of apoptosis. a: ActiveCaspase-3-positive cells were visualized by immunohistochemistry (Upperpanel—black arrows highlighting positive +4 cells following 1Gyirradiation; Lower panel-white arrows highlighting positive CBC cellsfollowing 10Gy irradiation). b: The frequency of positive cells percrypt was determined by counting three classes: CBC cells (locatedbetween the Paneth cells), +4 cells (located directly above the Panethcells) and TA cells: located at position 5-15. Maximal apoptosis at +4is already reached at 1 Gy while 10 Gy causes significantly moreapoptosis than 1 Gy irradiation in CBC cells.

FIG. 8. Whole mount analysis of LacZ expression in small intestine ofGPR49-EGFP-Ires-CreERT2 knock-in mice crossed with Rosa26-LacZ reportermice at the indicated time points following Tamoxifen injection a:1 daypost-induction. b: 5 days post-induction. c: 60 days post-induction.

FIG. 9. Colocalisation of proliferation marker Ki67 and GFP-positive CBCcells in the intestinal crypts of GPR49-EGFP-CreERT2 mice (serialsections).

FIG. 10. Sequences of the human, mouse and rat receptors.

FIG. 11. Predicted structure of Lgr4, 5 and 6.

FIG. 12. Restricted expression of a GPR49-LacZ reporter gene in adultmice Expression of GPR491acZ in selected adult mouse tissues. LGR5 isrestricted to rare cell populations in the brain (glomeruli of theolfactory bulb and several other poorly defined regions) (A), the eye(inner nuclear layer of the retina) (B), liver (cells surrounding theportal triads) (C) and adrenal gland (D)

FIG. 13. Lineage tracing in the stomach Lgr5-EGFP-CreERT2 mice werecrossed with Rosa26R reporter mice and Cre enzyme activity induced inthe LGR5+ve cells by IP injection of Tamoxifen. LacZ reporter geneactivity is initially restricted to the LGR5 cells (A), but rapidlyexpands to include the entire epithelium in the Stomach over time (B).This “lineage tracing” is maintained over long periods of time (B). Thisdemonstrates that all epithelial cells are derived from the LGR5+vepopulation in this tissue, proving that they are stem cells.

FIG. 14. Lineage tracing in the mammary gland Lgr5-EGFP-CreERT2 micewere crossed with Rosa26R reporter mice and Cre enzyme activity inducedin the LGR5+ve cells by IP injection of Tamoxifen. LacZ reporter geneactivity is initially restricted to the LGR5 cells (A), but expands toinclude the myoepithelium of newly-formed milk glands in lactatingfemales (B), indicating that LGR5 is specifically marking myoepithelialstem cells in this organ.

FIG. 15. Lineage tracing in the adrenal gland. Lgr5-EGFP-CreERT2 micewere crossed with Rosa26R reporter mice and Cre enzyme activity inducedin the LGR5+ve cells by IP injection of Tamoxifen. LacZ reporter geneactivity is initially restricted to the LGR5 cells (A), but expands toinclude the medulla of the adrenal gland (B), indicating that LGR5 isspecifically marking adrenal medulla stem cells.

FIG. 16. Lgr6 is expressed in cells of the upper bulge area of the mousehair follicle and in basal cells of the epidermis. Skin sections ofappr. 26 days old Lgr6-EGFP-Ires-CreERT2 mice (early anagen) wereobtained and stained for nuclear DNA (Topro) and EGFP visualized usingconfocal microscopy (A-C). During early anagen Lgr6 is expressed in theupper bulge (A, C) and the basal epidermis (A, B).

FIG. 17. The progeny of Lgr6+ cells contribute to all structures of thehair follicles (HF), interfollicular epidermis (IFE) and sebaceousglands (SG). To trace the progeny of Lgr6+ cellsLgr6-EGFP-Ires-CreERT2/ROSA26-LacZ mice were injected with tamoxifen(TM) at P20 when HFs are in telogen (A). At P23 a first staining in theIFE and HFs was detected (B). Analysis of LacZ staining progeny at P38(1st anagen, C, D) and P52 (2nd telogen, E, F) revealed contribution toall parts of the HFs, IFEs and SGs.

FIG. 18. The progeny of Lgr6+ cells contribute to the myoepithelium ofthe lung. To trace the progeny of Lgr6+ cellsLgr6-EGFP-Ires-CreERT2/ROSA26-LacZ mice were injected with tamoxifen(TM) at P20. Analysis of LacZ staining progeny at P38 (A, 10×, 20× and40× magnification from left to right) and P52 (B, 10×, 20× and 40×magnification from left to right) revealed contribution to themyoepithelium underlying the bronchioles of the lung.

FIG. 19. Low-dose oral induction with ß-NF does not induce Cre-mediateddeletion in stem cells of AHCre mice. Intestinal whole-mounts stainedfor ß-galactosidase from AhCre+ Rosa26R+ mice. a: No activation of theRosa-lacZ reporter gene is observed in intestines from non-inducedAhCre+ Rosa26R+ mice. b: Readily visible expression of lacZ throughoutthe intestine 2 days after a single gavage of 1 mg/kg ß-napthoflavone,indicating efficient Cre-mediated activation of the lacZ reporter. NolacZ expression is visible at the crypt base (lower panel) demonstratingthe absence of Cre-mediated recombination at the crypt base. c: NolacZ-positive crypt/villus units are visible on whole-mount intestines100 days post-induction, indicating that this dosing regime very rarelycauses recombination within the intestinal stem cells.

FIG. 20. Transformation of non-stem cells through loss of APC does notefficiently drive adenoma formation over extended time-periods. a-c:ß-catenin IHC performed on intestinal sections from AhCre+ Rosa26R+Apcfl/fl 3 days following a single gavage of 1.0 mg/kg ß-napthoflavone.Clusters of transformed cells with nuclear ß-catenin were frequentlyobserved on the villus (a) and upper regions of the crypt (b).ß-cateninhigh clusters were only very rarely observed at the crypt base(c). These clusters are highlighted with black arrows. d: Quantificationof the location of the ß-cateninhigh cell clusters on intestinalsections from AhCre+ Rosa26R+ Apcfl/fl 4 days following a single gavageof 1.0 mg/kg ß-napthoflavone. Box-plots showing numbers of foci observedat the crypt base, the upper crypt and the villus in 1600 crypt-villusunits. Significantly more clusters were seen at the upper regions of thecrypt than any other region (p=0.04, Mann Whitney, n=3). Nuclearß-catenin foci were observed only very rarely at the crypt base.e:□—ß-catenin IHC performed on intestinal section from AhCre+ Rosa26R+Apcfl/fl 24 days following a single gavage of 1.0 mg/kg ß-napthoflavone.Here, nuclear ß-catenin is seen in a small lesion 24 days after creinduction. f,g: ß-catenin IHC performed on intestinal section fromAhCre+ Rosa26R+ Apcfl/fl 167 days following a single gavage of 1.0 mg/kgß-napthoflavone showing a microadenoma (f) and small adenoma (g) withnuclear ß-catenin. h: Quantification of adenoma formation over extendedtime-periods in AhCre+ Rosa26R+ Apcfl/fl following a single gavage of1.0 mg/kg ß-napthoflavone. Lesion size was scored on intestinalwhole-mounts from AhCre+ Rosa26R+ Apcfl/fl mice that had been stainedfor lacZ to help visualise the small lesions (at least 3 mice were usedfor each time-point). No adenomas were seen in mice up to and includingday 24 and there was only the very rare microadenoma in mice at day 24.The occasional adenoma was observed in AhCre+ Rosa26R+ Apcfl/fl at 100days (plus), however the majority of lesion remained microscopic showingthat most lesions were not progressing to adenoma despite a long latencyperiod.

FIG. 21. Lgr5+ve intestinal stem cells transformed following loss of APCpersist and fuel the rapid formation of ß-cateninhigh microadenomas.a-i: The consequences of Lgr5+ve intestinal stem cell transformation andtheir subsequent fate was tracked over an eight day period usingß-catenin and GFP as markers of transformed cells and Lgr5+ve stem cellsrespectively. a-c: Accumulation of the Wnt effector, ß-catenin is firstobserved in scattered Lgr5+ve stem cells 3 days after Cre induction inLgr5-EGFP-Ires-CreERT2/APCfl/fl intestines. Representative examples ofß-cateninhigh Lgr5+ve stem cells are circled. d-f: Five dayspost-induction the transformed Lgr5-GFP+ve stem cells remain (e,f: blackarrows) and are associated with clusters of transformed (ß-cateninhigh)cells within the TA compartment. g-h: Eight days post-induction theclusters of transformed cells have expanded to fill the TA compartment(h: red circle). The transformed Lgr5-GFP+ve stem cells at the cryptbase persist (h,i: black arrows), but their transformed progeny withinthe TA compartment are Lgr5-GFP-ve. (h,i: red circles).

FIG. 22. Selective transformation of Lgr5+ve stem cells following lossof APC efficiently drives adenoma formation throughout the smallintestine. a-h: The appearance and development of intestinal adenomasand the expression of the Lgr5-GFP stem cell marker within theseadenomas was tracked over a 36 day period using GFP (f) and ß-catenin(all others) IHC.a-b: Multiple small adenomas are readily visiblethroughout the intestine 14 days after Lgr5+ve stem cell transformation.c-f: Multiple macroscopic adenomas (>100) are present after 24 days.Lgr5-GFP expression in adenomas is restricted to rare scattered cells(f; circled). g,h: At 36 days, a large proportion of the intestine isfilled with macroscopic adenomas.

FIG. 23. Presence of Lgr5+ stem cells in intestinal adenomas. Intestinaladenomas express high levels of ß-catenin as a result of chronicactivation of the Wnt pathway (A). In contrast to other Wnt target geneswhich are highly expressed throughout the adenoma (not shown),expression of the intestinal stem cell marker Lgr5-GFP is restricted toscattered cells with characteristic stem cell morphology: slender,comma-shaped cells; indicated with black arrow (B). We speculate thatthese Lgr5+ve cells within the adenoma are stem cells dedicated tomaintaining the growth of the adenoma (so-called cancer stem cells).

FIG. 24. FACS analyses of LGR5 expression in L8 cells, which are clonalderivatives of LS174T cells, which express dominant negative Tcf4(DNTcf4) upon Doxycycline (DOX). DNTcf4 turns off constitutive activeWnt pathway. After 48 hrs of DOX induction, a reduction in hLgr5 proteinlevels is observed. Rat IgG is used as negative isotype control. 9G5 isa rat monoclonal derived antibody directed against hLgr5

FIG. 25. Comparison of Lgr5+ stem cells and their direct progeny.GFP-positive epithelial cells from cell suspensions prepared fromfreshly isolated crypts of Lgr5-EGFP-ires-CreERT2 mice. FACS analysisdistinguished a GFP-high (GFPhi) and a GFP-low (GFPlo) population, whichwe tentatively identified as CBC cells and their immediatetransit-amplifying daughters, respectively (A). An example of aWnt-responsive gene, Sox9, which shows high level expression in CBCcells, but TA cells directly above the Paneth cells also express thisgene in in situ hybridizations, albeit at a much lower level (B).

FIG. 26. Endogenous hLgr5 staining of a human colon cancer cell line(L8) using several Lgr5-specific monoclonal antibodies. L8 cells are aclonal derivative of the parental LS174T cell-line. FollowingDoxycycline (DOX) induction the L8 cells express a dominant-negativeform of Tcf-4 (DNTcf4). DNTcf4 efficiently blocks the constitutive Wntpathway activity in these cells and consequently switches off Tcf targetgenes. After 48 hrs of DOX induction a major reduction in hLgr5 proteinlevels is observed. Rat IgG is used as negative isotype control.

FIG. 27. Light chain+heavy chain sequences analyzed using KABAT method.CDR regions are in bold and in italics.

EXAMPLES Example 1 Experimental Part

Northern blotting and induced Wnt pathway inhibition in LS174T clone L8:As in van de Wetering, M. et al. The beta-catenin/TCF-4 complex imposesa crypt progenitor phenotype on colorectal cancer cells. Cell 111,241-50 (2002). The probe spanned the entire reading frame of mouseGpr49. Crypt and villus epithelial preparations for RNA isolation weregenerated from 0.5 cm lengths of intestine by 4 successive rounds ofincubation in pre-warmed 30 mM EDTA at 37° C. for 10 minutes, followedby vigorous shaking (10×) in ice-cold PBS. Fractions 1 and 4, comprisingpredominantly villi and crypts respectively were used for RNA isolation.

Mice: GPR49-LacZ mice were generated by homologous recombination in EScells targeting an Ires-LacZ cassette to the 5′ end of the last exon,essentially removing the region containing all TM regions and creating anull allele (Lexicon). GPR49-EGFP-Ires-CreERT2 mice were generated byhomologous recombination in ES cells targeting an EGFP-Ires-CreERT2cassette to the ATG of GPR49. Rosa26-lacZ Cre reporter mice wereobtained from Jackson Labs.

Tamoxifen induction: Mice of at least 8 weeks of age were injected onceintraperitoneally with 200 μl of Tamoxifen in sunflower oil at 10 mg/ml.BrdU injection: Mice were injected intraperitoneally at four hourintervals with 200 μl of a BrdU solution in PBS at 5 mg/ml.

Immuno Electron Microscopy: Intestines were dissected and perfuse-fixedin 4% PFA in 0.2 M PHEM-buffer, embedded in gelatine, cryosectioned witha Leica FCS cryoultratome and immunolabelled against GFP with polyclonalrabbit anti-GFP antibody. Samples were trimmed using a diamond Cryotrim90 knife at −100° C. (Diatome, Switzerland) and ultrathin sections of 70nm were cut at −120° C. using a Cryoimmuno knife (Diatome, Switzerland).For the low magnification EM images the 15 nm protein A-gold particles(UMCU, Utrecht, The Netherlands) were briefly silver enhanced withR-GENT SE-EM (Aurion, The Netherlands) according to the manufacturersinstructions. Aspecific binding to Paneth cell granules was diminishedby applying Blocking solution (Aurion, The Netherlands) prior to theprimary antibody.

Tissue sample preparation for immunohistochemistry, in-situhybridization and LacZ expression analysis: All performed as previouslydescribed in Muncan, V. et al. Rapid loss of intestinal crypts uponconditional deletion of the Wnt/Tcf-4 target gene c-Myc. Mol Cell Biol26, 8418-26 (2006). In-situ probes comprising a 1 kb N-terminal fragmentof mGPR49 were generated from sequence-verified Image Clone 30873333.Ki67 antibodies were purchased from Monosan (The Netherlands),Phospho-histone H3 from Campro Scientific (The Netherlands),anti-synaptophysin from Dako, anti BrdU from Roche. Polyclonal rabbitanti-GFP was provided by Edwin Cuppen, Hubrecht Institute.

Generation of Suspension of Human (Tumor) Tissue Cells.

Using a razor blade, mince freshly isolated human (tumor) tissue as muchas possible. Do this in serum-free media. Draw minced tumor into a 25 mlpipette. Place the solution into a 50 ml conical tube. Incubate at 37 Cfor 30-60 min after adding collagenase IV (200 units/ml) (Sigma). Thefinal concentration should be 200 units/ml. Pipette up and down a fewtimes every 10 min (approx). Pass the solution through a filter (45micrometer pore size; Becton Dickinson). Wash the filter with 4-5 ml ofserum-free medium. Centrifuge the solution @ 1500 rpm for 10 min (4° C.)Resuspend the pellet in hypotonic ammonium chloride (approx. 5 ml).Leave 10 min at room temperature (this will lyse red blood cells). Thenadd equal volume of serum-free media and centrifuge again. Resuspendpellet in serum free medium. If clumpy then pass through another filter.Count with trypan blue to see the percent dead cells.

Cancer Stem Cell Assay by Xenografting in Immunodeficient Mice

The mice are sublethally irradiated with 320 Rad. The experimentalprocedure involves injecting human (colon) cancer cell suspensions underthe renal capsule of NOD/SCID mice. The mice are handled using steriletechniques and anaesthetized using inhalational anaesthesia: isoflurane.The mice are placed on a heating pad during the procedure.

A clipper is used to shave the abdomen, which is then preppedsequentially with: (1) iodine based solution and (2) 70% ethanolsolution. The area is then dabbed with a gauze. The mouse is placed onits side (left side up). A 1 cm (approximately) flank incision is madewith scissors, just below the costal margin on the left side. Deliverthe kidney into the wound. The cell suspension to be assayed for cancerstem cell activity is mixed 1:1 (medium: Matrigel) on ice. Utilizing atuberculin syringe, inject 25 microliter of the cell suspension underthe renal capsule. Deliver the kidney back into the abdomen. If cancerstem cell activity is present in the cell suspension, a tumor will growout in the subsequent weeks/months which is analysed by histology andshould resemble the original human tumor.

The intestinal epithelium is the most rapidly self-renewing tissue inadult mammals. Current models state that 4-6 crypt stem cells reside atthe +4 position immediately above the Paneth cells in the smallintestine; colon stem cells remain undefined. Gpr49/Lgr5 was selectedfrom a panel of intestinal Wnt target genes for its restricted cryptexpression. Two knock-in alleles revealed exclusive expression of Gpr49in cycling, columnar cells at the crypt base. In addition, Gpr49 wasexpressed in rare cells in several other tissues including stomach,breast and hair follicle. Using an inducible Cre knock-in allele and theRosa26-LacZ reporter strain, lineage tracing experiments were performedin adult mice. The Gpr49^(+ve) crypt base columnar cell (CBC) generatedall epithelial lineages over a 60-day period, implying that itrepresents the stem cell of the small intestine and colon. Theexpression pattern of Gpr49 shows that it marks stem cells in multipleadult tissues and cancers.

The absorptive epithelium of the small intestine is ordered into cryptsand villi¹ (References 2). In the mouse, the small intestinal epitheliumturns over every 3-5 days. The massive rate of cell production in thecrypts is balanced by apoptosis at the tips of the villi. To date,intestinal stem cells have not been functionally identified, due to thelack of unique markers and the absence of stem cell assays. The analysisof mouse chimeras and mutagen-induced somatic clones^(2, 3) (References2) and the study of regeneration upon injury have allowed an operationaldefinition of stem cell characteristics. Stem cells are believed tocycle steadily to produce the rapidly proliferating transit amplifying(TA) cells capable of differentiating towards all lineages. Stem cellsself-renew throughout life, and regenerate the epithelium followinginjury. The estimated number of stem cells is between 4 and 6 per crypt²(References 2). Long-term DNA label retention has tentatively locatedstem cells at “position +4” directly above the Paneth cells⁴ (References2). Three differentiated cell types (enterocytes, goblet cells andenteroendocrine cells) form from TA cells at the crypt-villus junctionand continue their migration in coherent bands stretching along thecrypt-villus axis. While crypts are monoclonal, each villus receivescells from multiple different crypts and is therefore polyclonal. Thefourth major differentiated cell-type, the Paneth cell, resides at thecrypt bottom. The colon epithelium contains crypts, but has a flatsurface rather than carrying villi. This epithelium comprises two majordifferentiated cell types: the absorptive colonocytes and the gobletcells' (References 2). To date, no stem cells have been identified inthe colon.

Since Wnt signals constitute the major driving force behind the biologyof the crypt⁵ (References 2), we hypothesized that one or moreWnt/Tcf4(Tcf712) target genes may be specifically expressed in the stemcells. We have previously described the Wnt/Tcf4 target gene program incolorectal cancer cells and found that it is physiologically expressedin intestinal crypts^(6, 7) (References 2). When we studied theexpression of approximately 80 selected Tcf4 target genes⁷, theoverwhelming majority was expressed either in Paneth cells or TA cells.The Gpr49/Lgr5 gene, however, was expressed in a unique fashion. TheGpr49 gene behaved as a Wnt target gene, as its expression wasextinguished upon the induced inhibition of Wnt pathway activity bydominant-negative TCF4 in the human colorectal cancer cell line LS174T,a cell system described earlier⁶ (References 2) (FIG. 1a , lane 1 vs.2). Accordingly, the gene was expressed in the crypts, but not thevilli, of mouse small intestine (FIG. 1a , lane 3 vs. 4). In situhybridization revealed expression in a limited number of cells locatedat all crypt bottoms as well as in adenomas in the small intestine of anAPC^(min) mouse (FIGS. 1b and c ). This expression pattern, enlarged inFIG. 2c , clearly differed from that obtained with a Panethcell-specific gene (FIG. 2a ) or a TA-specific gene (FIG. 2b ). TheGpr49 gene appeared to mark small cells interspersed between Panethcells, the cycling Crypt Base Columnar (CBC) cells (FIG. 2d-h ; seebelow).

Gpr49 encodes an orphan G protein-coupled receptor (GPCR), characterizedby a large leucine-rich extracellular domain. It is closely related toGPCRs with glycoprotein ligands, such as the TSH-, FSH- andLH-receptors⁸ (References 2). Gpr49 was on our original list of Tcf4targets in colorectal cancer⁶, but has since been observed to beoverexpressed also in ovarian and hepatocellular carcinomas^(9, 10)(References 2). In order to study its expression in detail we obtained aknock-in allele, in which LacZ, preceded by an internal ribosome entrysite (ires), is integrated just N-terminal to the first transmembranedomain essentially creating a null allele (FIG. 3a ).

While our study was in progress, Morita et al published the Gpr49^(−/−)phenotype¹¹ (References 2). A malformation of the tongue and lower jawcauses newborn mutants to swallow large amounts of air leading to theirdemise soon after birth. We observed the same phenotype in our mice. Ofnote, crypts and intestinal stem cells are first established severalweeks after birth¹² (References 2). The heterozygous Gpr49-LacZ miceallowed us to detail the expression of Gpr49. Before birth, a dynamicand complex expression pattern was observed (Barker et al, inpreparation). Around birth, Gpr49 expression subsided in virtually alltissues. Expression in adult mice was restricted to rare, scatteredcells in the eye, brain, hair follicle, mammary gland, reproductiveorgans, stomach and intestinal tract (FIG. 3, and not shown). In thesmall intestine, Gpr49 expression was observed in slender cells locatedbetween the Paneth cells in the small intestine (FIGS. 3b and c ) and ina similar number of cells at the bottom of colon crypts (FIGS. 3d and e). Counting of blue cells in small intestinal crypts sectioned throughthe lumen revealed the presence of approximately 3.5 of such cells persectioned crypt (FIG. 2i , white bar). More than 30 years ago, Leblondand Cheng noted the presence of cycling cells between the Paneth cellsand have coined the term “Crypt Base Columnar” (CBC) cells¹³ (References2). Based on their position and their presence in long-term mutantepithelial clones, Cheng and Bjerknes^(2, 14) (References 2) and Gordonand colleagues¹⁵ (References 2) have proposed that these cells mayharbor stem cell activity

By morphology, the slender Gpr49^(+ve) CBC cells with their scantcytoplasm and flat, wedge-shaped nuclei pointing towards the crypt lumenwere readily distinguishable from the adjacent Paneth cells.Occasionally (once in approximately every ten crypts), these cells alsoexpressed the M phase marker phospho-histone H3, indicating that thecells are in cycle (FIG. 2f ). Indeed, a 4 hour pulse of BrdU labeledapproximately 1 of these cells per crypt (FIGS. 2G and 2I, left blackbar), while a 24 hour continuous BrdU labeling resulted in more than 3positive cells per crypt (FIGS. 2h and i , right black bar), close tothe total number of CBC cells per crypt (FIG. 2i , white bar). Thisobservation implied that the average cycling time of CBC cells is in theorder of 1 day. Direct colocalization of the proliferation marker Ki67with GPR49-LacZ further confirmed that the LacZ positive CBC cells aretypically cycling (FIG. 2e and FIG. 9).

In order to be able to visualize live CBC cells and to study theirpotential “sternness”, we generated another knock-in allele, in which weintegrated an EGFP-ires-CreERT2 cassette at the first ATG codon of Gpr49(FIG. 4a and FIG. 6). Heterozygous mice carrying this allele werehealthy and fertile. The GFP pattern observed in adult tissuesfaithfully recapitulated the pattern previously seen with the Gpr49-LacZallele in eye, brain, hair follicle, mammary gland, reproductive organs,stomach and intestinal tract (not shown, and FIG. 4). Confocal imagingallowed the visualization of the Gpr49^(+ve) cells by GFP fluorescencein small intestine (FIG. 4 b,c,e) and colon (FIG. 4f ). Immuno-ElectronMicroscopy using immunogold labeling of the GFP-positive CBC cells andof neighbouring Paneth cells and fibroblasts illustrated the uniqueultrastructural anatomy of the CBC cells (FIGS. 4g and h ). Typically,the CBC cells were relatively broad at their base, contained a flatwedge-shaped nucleus and scarce organelles. A slender extension ofapical cytoplasm was squeezed inbetween neighboring endoplasmicreticulum- and granule-rich Paneth cells, extended to the crypt lumenand carried some apical microvilli.

We then crossed the EGFP-ires-CreERT2 knock-in allele with theCre-activatable Rosa26-LacZ reporter¹⁶ (See FIG. 4a for experimentalstrategy). Injection of Tamoxifen activates the CreERT2 fusion enzyme inGpr49-expressing cells. Cre-mediated excision of the roadblock sequencein the Rosa26-LacZ reporter should then irreversibly mark theGpr49^(+ve) cells. Moreover, while potential progeny of these cells willno longer express GFP, the activated LacZ reporter should act as agenetic mark, facilitating lineage tracing.

LacZ expression was not observed in non-induced mice (not shown). Toquantify the total number of CBC cells per crypt in which the latent Creenzyme could be activated by Tamoxifen, we treated 2-3 months-old micewith Tamoxifen and sacrificed the mice 12 hours later. As evident inFIG. 5a , blue LacZ signals appeared at the typical CBC positions. Wedetermined the frequency at which the blue cells appeared at specificpositions relative to the crypt bottom, according to the scheme in FIG.5b . The large majority of the Cre^(+ve), LacZ-labelled CBC cellsoccurred at positions between the Paneth cells, while only 10% of thesecells were observed at the +4 position directly above the cells (FIG. 5b, blue line). Quantitative data on the position of long term DNAlabel-retaining cells obtained in adult mice post-irradiation (markingthe “+4” intestinal stem cell) were published recently by Potten andcolleagues¹⁷. Comparison of these data (FIG. 5b , red line) with theposition of CBC cells with activatable Cre revealed that the two markersidentified largely non-overlapping cell populations.

Another defining characteristic of the +4 cell is their exquisitesensitivity to low dose (<1Gy) radiation⁴. To compare relative radiationsensitivity between CBC cells and +4 cells, adult mice were irradiatedwith 1 Gy or 10 Gy and subsequently sacrificed 6 hours later, at thepeak of apoptosis. Active Caspase-3-positive cells were visualized byimmunohistochemistry (FIG. 7a ). The frequency of positive cells percrypt was determined by counting apoptotic cells in three classes: CBCcells (defined by their location between the Paneth cells), +4 cells(located directly above the Paneth cells) and TA cells: located atposition 5-15 (FIG. 7b ). Maximal apoptosis at the +4 position wasalready reached at 1 Gy (a: upper panel, black arrows) in concordancewith⁴ (References 2), while 10 Gy caused significantly more apoptosisthan 1 Gy irradiation in CBC (a: lower panel) and TA cells, confirmingthe different identities of the CBC and +4 cells.

Adult mice were then subjected to a Tamoxifen pulse and were sacrificedat 1, 5, 12 (not shown) and 60 days post-induction. One daypost-induction, occasional CBC cells in the crypts of small intestineand colon were observed to express LacZ (FIGS. 5c and 5i respectively).As is demonstrated for whole-mount small intestine in FIG. 8, parallelribbons of cells emanated from the crypt bottoms and ran up the side ofadjacent villi at later time points. The kinetics of stripe formationwas not uniform. Some stripes already reached the villus tips 5 dayspost-induction, while blue staining in occasional crypts was stillrestricted to crypts. At 5 days post-induction (FIG. 5d ), suchcrypt-restricted expression was very rarely seen. The CBC cells werecapable of long-term maintenance of the self-renewing epithelium, sincein 60-day intestines (FIG. 5e and FIG. 8) the frequency of blue cryptsand ribbons was essentially identical to that seen at 5-12 dayspost-induction.

Double-labeling of 60 day-induced intestine demonstrated the presence ofPAS-positive goblet cells (FIG. 5f ), PAS-positive Paneth cells (FIG. 5g) and synaptophysin-positive enteroendocrine cells (FIG. 5h ) in theLacZ-stained clones originating from the GPR49^(+ve) CBC cells. Usingmutational marking, Cheng and Bjerknes have reported the existence ofdifferent types of long-lived epithelial clones, i.e. columnar(enterocyte) clones, mucous (goblet) clones and mixed clones². Theclones observed in our study were exclusively of the mixed variety. Inblue clones, the frequency of goblet cells (114 out of 2043 total cellscounted), enterocytes (1846/2043) and Paneth cells (83/2043) wascomparable to the frequency of goblet cells (127 out of 3691 total cellscounted), enterocytes (3345/3691) and Paneth cells (127/3691) inunmarked adjacent epithelium. As noted² (References 2), the thirdsecretory cell type, the enteroendocrine cell, was too rare to allowaccurate enumeration. Taken together, we conclude that the Gpr49^(+ve)CBC cells represent the genuine stem cells of the small intestine.

Analysis of the colon yielded essentially identical observations. TheGpr49^(+ve) cells yielded blue clones emanating from the crypt bottom(FIG. 5i ). These clones contained colonocytes as well as goblet cells,and essentially remained unchanged during the 60 days of chase (FIG.5j,k ). One significant difference with the situation in the smallintestine involved the kinetics of clone-formation. At 5 days, bluestaining in most crypts was still restricted to the bottom and entirelyblue crypts were only rarely observed, implying that the colon stemcells were more often quiescent than their small intestinalcounterparts. At later days, the relative number of entirely blue cryptsincreased. We concluded that the Gpr49^(+ve) colon cells fulfilled thestem cell requirements in being pluripotent and capable of maintainingepithelial self-renewal over long periods of time.

Our observations provide the definitive characterization of theintestinal stem cell by lineage tracing using the expression of a singlemarker gene, Gpr49. The small intestinal Gpr49^(+ve) cells are generallynot quiescent, but are rapidly cycling, as evidenced by the expressionof Ki67 and phospho-histone H3, the incorporation of BrdU, and by thekinetics of ribbon formation. Gpr49^(+ve) cells of the small intestineappear more actively dividing than their colonic counterparts, likelyreflecting differences in the rate of epithelial turnover between thetwo organs. It appears somewhat counterintuitive that stem cells cycle.This is, however, not unprecedented. Germ stem cells in the Drosophilatestis and ovary of the fly, arguably the best understood adult stemcells in animals, cycle throughout the lifetime of the adult fly¹⁸(References 2). Similarly, a recent elegant study demonstrated thatadult stem cells of mammalian skin are continuously cycling¹⁹(References 2).

The cycling +4 cells have previously been proposed by Potten andcolleagues to represent the small intestinal stem cells⁴ (References 2),a notion not confirmed here. The notion was based on the observationthat a DNA label incorporated during periods of high stem cell activitywas specifically retained in cells at the +4 position. Long-term labelretention is often used as an indirect strategy to identify stem cells¹²(References 2). It should be noted, however, that terminallydifferentiating cells will also retain DNA labels and that labelretention should therefore be interpreted with caution. Previous studieshave proposed other markers for intestinal stem cells. Musashi^(20, 21)(References 2) and CD133²² (References 2) in our hands stain up to 30-50cells per crypt (not shown), which appear to encompass CBC cells as wellas early transit amplifying cells. Li and colleagues have describedseveral molecular markers for the +4 cells, including phospho-PTEN,phospho-AKT and 14-3-ζ²³ (References 2). Our current study implies thatthe validity of these putative stem cell markers should be reconsidered.

It appears rather unique that adult stem cells can be identified basedon the expression of a single gene. This phenomenon may not berestricted to the intestine, since we observe highly restricted Gpr49expression in a variety of other tissues. In the anagen hair follicle,the Gpr49 gene is expressed in the bulge area as well as in the outerroot sheath (FIG. 3i ). While quiescent LTR stem cells resideexclusively in the bulge, activated stem cells migrate down through theouter root sheath towards the basal papilla²⁴⁻²⁶ (References 2). Indeed,Gpr49 was recently reported to be the second most highly upregulatedgene as assessed by differential expression arraying on isolated hairfollicle stem cells²⁷ (References 2). Moreover, preliminary lineagetracing experiments in the hair follicle support the notion thatGpr49^(+ve) cells represent stem cells (Barker, Clevers and Toftgard,unpublished). While patterns of proliferation in stomach glands haveindicated that the epithelial stem cells reside at the isthmus, halfwaybetween the gland base and epithelial surface²⁸ (References 2) we findGpr49 expressed at gland bottoms (FIG. 3f,g ). Ongoing lineage tracingexperiments imply that the entire glands derive from these cells (Barkerand Clevers, unpublished). In the mammary gland, stem cells reside inthe basal epithelial layer²⁹ (References 2), where we observe Gpr49expression (FIG. 3h ). Gpr49 may thus represent a more general marker ofadult stem cells. If true, the mouse models developed in the course ofthis study will allow the isolation as well as specific geneticmodification of live adult stem cells in a variety of organs. We firstidentified Gpr49 as a gene expressed in colon cancer cells⁶ (References2). It is expressed in other cancers^(9, 10) (References 2) and, asdescribed in the current study, also in premalignant mouse adenomas.Based on the observations reported here, we now know that Gpr49 may markcancer stem cells (“tumor-initiating cells”) in colorectaladenocarcinomas.

Example 2 Lgr5 Tissue Expression and Evidence for Lgr5⁺ Stem Cells inthese Tissues

Materials and Methods

For experimental details, we refer to materials and methods as used inexample 1

Results and Discussion

Lgr5 Expression Also Detected in Brain, Retina, Liver and Adrenal Gland

We studied the Lgr5 expression in multiple other tissues in the micecarrying lacZ integrated into the last exon of the Gpr49 gene, removingall transmembrane regions of the encoded Gpr49 protein. We determinedthat, analogous to colon and small intestine, Lgr5⁺ cells were detectedin brain, retina, liver and adrenal gland (FIG. 12). In adult mice, LGR5is restricted to rare cell populations in the brain (glomeruli of theolfactory bulb and several other poorly defined regions), the eye (innernuclear layer of the retina), liver (cells surrounding the portaltriads) and adrenal gland.

Lineage Tracing in the Stomach, Mammary Gland and Adrenal Gland Provesthat Lgr5 is Marking Stem Cell Populations in these Tissues

We used the LGR5KI/Rosa26-lacZ mice¹⁶ (See example 1 for experimentalstrategy) to study the presence of Lgr5⁺ stem cells in multiple othertissues. Injection of Tamoxifen activates the CreERT2 fusion enzyme inGpr49-expressing cells. Cre-mediated excision of the roadblock sequencein the Rosa26-LacZ reporter should then irreversibly mark theGpr49^(+ve) cells. Moreover, while potential progeny of these cells willno longer express GFP, the activated LacZ reporter should act as apermanent genetic mark, which will be passed on to any descendents ofthe LGR5+ve cells, allowing us to track their appearance and fatein-vivo.

Lineage tracing was initiated in young LGR5KI/Rosa26-lacZ mice and thestomach epithelium analyzed for LacZ activity after 6 months. LGR5-lacZpositive cells are initially restricted to the base of the glands (FIG.13a ). After 6 months, multiple entirely lacZ-positive glands arevisible throughout the stomach (FIG. 13b ), demonstrating that theLGR5+ve cells are capable of generating all cell-types on the glandularepithelium over long periods of time.

Similar lineage tracing experiments were performed and the mammary glandepithelium analyzed for LacZ activity over a 3 month period. LGR5-lacZpositive cells are initially restricted to rare basal epithelial cellson virgin glands (FIG. 14a ). Following pregnancy, LacZ-positive cellsare visible in the basal epithelium of the newly-formed milk glands(FIG. 14b ). This demonstrates that LGR5⁺ cells in the mammary gland aremyoepithelial stem cells.

Lineage tracing in the adrenal glands analyzed for LacZ activity over a3 month period. LGR5-lacZ positive cells are initially restricted to theperiphery of the adrenal gland 5 days after induction (FIG. 15a ). After3 months the majority of the adrenal medulla is LacZ positive (FIG. 15b). This remains positive over a 14 month period (not shown). Thisdemonstrates that the LGR5⁺ cells are the stem cells of the adrenalmedulla.

Example 3 Lgr6 Tissue Expression and Lgr6 Expression in Related StemCells

Material and Methods

Transgenic Mice and Treatments.

Lgr6-EGFP-Ires-CreERT2 mice were generated by homologous recombinationin embryonic stem cells targeting an EGFP-Ires-CreERT2 cassette to theATG of Lgr6. Rosa26-LacZ reporter mice were obtained from the Jacksonlaboratory. Mice were fed ad libitum. The Cre recombinase was activatedin Lgr6-EGFP-Ires-CreERT2/Rosa26-LacZ mice by injecting 200 μl oftamoxifen (10 mg/ml dissolved in sunflower oil) intraperitoneally.

Confocal Analysis of EGFP Expression

For confocal imaging the skin samples were fixed in formalin for 15minutes at RT and embedded in 4% low melting agarose. Longitudinalsections between 100 and 200 μM thick were prepared using a vibratome.Sections were then permeabilized in PBS supplemented with 1% BSA+1%DMSO+0.1% TritonX, stained for 30 minutes with TO-PRO 1:1000 dilution(Molecular Probes) and embedded using Vectashield (Vector Labs).Sections were imaged with a Sp2 confocal microscope (Leica) andprocessed using Volocity and Photoshop CS2 software.

Detection of Beta-Galactosidase Activity

Freshly obtained tissues were fixed for 2 hours in 1% Formaldehyde/0.2%glutaraldehyde/0.02% NP40 in PBS0 solution at 4° C. on a rollingplatform. Samples were washed 3 times for 20 min with rinse buffer (2 mMMgCl₂/0.02% NP40/PBS0) and stained for 36-48 h in a solution consistingof 1 mg/ml X-gal, 5 mM ferrothiocyanide, 5 mM ferrithiocyanide, 0.1%sodium deoxycholate in rinse buffer. The substrate was removed and thesamples washed twice in PBS0 for 20 min at room temperature on a rollingplatform. The tissues were then fixed overnight in 4% PFA in PBS0 at 4°C. in the dark on a rolling platform. The PFA was removed and thetissues washed twice in PBS0 for 20 min at room temperature. The sampleswere embedded in paraffin, sectioned (4 μm) and counterstained withneutral red.

Results and Discussion

To characterize the expression of Lgr6 in the skin we utilized aknock-in mouse, where the Lgr6 promoter controls the expression of EGFPand the CreERT2 fusion protein, termed Lgr6-EGFP-Ires-CreERT2. At P25when the hair follicles (HFs) are in the growing (anagen) phase, theGFP-positive cells were localized to cells of the upper bulge/isthmusarea of the HF (FIG. 16A, C) and basal cells of the interfollicularepidermis (IFE, FIG. 16A, B). This expression pattern suggests that Lgr6expression marks a SC/early progenitor cell population of the hairfollicle and the epidermis.

To address the question whether the Lgr6⁺ cells of the anagen HF and IFErepresent functional stem cells 20 day-oldLgr6-EGFP-Ires-CreERT2/Rosa26-LacZ mice were injected with tamoxifen. AtP20 Lgr6 is expressed in the upper bulge/isthmus area of the HF andbasal cells of the IFE (data not shown). Three days post tamoxifeninjection a scattered pattern of labeled cells could be seen in the HFsand the IFE (FIG. 17B). At 18 days post-injection the progeny of Lgr6⁺cells could be seen in the anagen HFs (FIG. 17C, D) as well as in theIFE and the sebaceous glands (SG) (FIG. 17C, D). In the next telogenlabeled cells were found in the bulge and isthmus of the HFs (FIG. 17E,F) and the IFE and SGs (FIG. 17E, F). This observation strongly suggeststhat Lgr6⁺ cells located in the bulge/isthmus area of the HF and thebasal IFE exhibit stem cell properties. In particular, Lgr6⁺ cells cancontribute to all the appendages of the skin, i.e. the growing HFs, theIFE and the SG.

It seems rather unique that adult stem cells can be identified on thebasis of expression of a single gene, in this case Lgr6. This phenomenonmay not be restricted to the skin, because we observe highly restrictedexpression of Lgr6 in a variety of other tissues. To address thequestion whether the Lgr6⁺ cells represent functional stem cells in anyother tissues 20 day-old Lgr6-EGFP-Ires-CreERT2/Rosa26-LacZ mice wereinjected with tamoxifen. LacZ staining was performed on 18 and 32 dayspost tamoxifen injection to assess for lineage tracing in a variety oftissues. Interestingly, LacZ positive cells were present in themyoepithelium underlying the bronchioles of the lung at both timepoints(FIG. 18). Thus, Lgr6⁺ cells contribute to the myoepithelium of the lungstrongly suggesting that Lgr6⁺ cells located in the lung exhibit stemcell properties as well.

Example 4 the Role of Lgr5⁺ Cancer Stem Cells in Adenoma

The anatomy of the intestinal crypt is uniquely suited to study adultstem cells in their niche. The epithelium of the murine small intestinerenews every five days^(1,2) (references 5). Vigorous proliferationoccurs within the crypt compartment. We have recently identifiedslender, undifferentiated cells expressing the Lgr5 gene located atcrypt bottoms as the stem cells of the small intestine and colon. Eachsmall intestinal crypt contains approximately 6 independent, long-livedstem cells that are intermingled with Paneth cells in the smallintestine and with goblet cells in the colon. Counter-intuitively, thesecells are not quiescent, but complete a cell cycle every day³(references 5). Leblond and colleagues have originally named these cellsmorphologically Crypt Base Columnar (CBC) cells^(4, 5) (references 5).Their daughter cells constitute the readily distinguishable transitamplifying (TA) crypt compartment. TA cells divide every 12-16 hours,generating some 300 cells per crypt every day⁶ (references 5).Newly-formed TA cells reside within crypts for approximately 48-72hours, undergoing up to 6 rounds of cell division while migratingupwards⁶ (references 5). When the committed TA cells reach thecrypt-villus junction, they rapidly and irreversibly differentiate. Theproliferation is balanced by apoptosis at the other end of theepithelial conveyor belt, the tip of the villus. Only Paneth cellsescape this flow; they have a residence time of 3-6 weeks at the cryptbase⁷⁻⁹ (references 5). Initiating mutation in intestinal malignanciesin mouse and man target components of the Wnt pathway, most frequentlythe negative Wnt regulator APC^(10, 11) (references 5). This results inthe constitutive activation of a Wnt target gene program that drives theformation of benign adenomas or polyps¹²⁻¹⁵ (references 5). However, itremains unclear which cell type sustains the cancer-initiating mutation.

The Cytochrome P450-promoter-driven AH-Cre mouse allows conditionaldeletion of foxed alleles in the intestinal epithelium followingadministration of the inducing agent, ß-Napthoflavone (B-NF).Importantly, the AH-Cre allele is highly active in all cell types of theepithelium, including the stem cells¹⁶ (references 5). We havepreviously employed a floxed allele of APC¹⁷ (references 5) incombination with the AH-Cre mouse line to demonstrate that acute loss ofAPC throughout the adult intestinal epithelium following IP injection ofß-NF leads to an immediate quantitative transformation of theepithelium¹⁶ (references 5), a process almost entirely dependent on thedownstream Wnt target gene c-Myc¹⁸ (references 5). High-dose oral ß-NFinduces more stochastic deletion of APC, resulting in rapid adenomaformation throughout the intestine within 3 weeks¹⁹ (references 5). Boththese high-dose induction protocols effect deletion in all compartmentsof the epithelium, including the stem cells at the crypt base.

Having validated the AHCre/APC^(flox/flox) mouse as an inducible modelof intestinal cancer, we sought to dissect the mechanism of adenomaformation by identifying its cell-of-origin. We reasoned that oraladministration of low-dose ß-NF would restrict its range of action tocells on the villi and the upper regions of the crypts. Carefultitration of the required dosage revealed that following oraladministration of 1 mg/kg ß-NF, the efficiency of Cre activation in thestem cells at the crypt base was extremely low, as measured by thenegligible frequency of long-term lineage tracing initiated inAHCre/R26R mice receiving this dose. This dose was still very efficientin inducing Cre activity in the TA compartment and villus epithelium, asdetected using the Rosa26-LacZ mouse²⁰ (references 5) as a Cre reporter(FIG. 19a, b ). In a typical experiment over 70% of villi contained bluecells 2 days after induction, but at day 7 blue staining could no longerbe detected. In line with this, no crypt/villus ribbons were detected atday 100 post-oral induction (FIG. 19c ).

Using this dosing regime on AHCre/APC^(flow/Flox)/R26R mice, multipleß-catenin^(high) foci/lesions rapidly became visible throughout theupper crypt and villus epithelium. Representative pictures taken at day3 post-induction are given in FIG. 20. Mutant APC foci evident by highß-catenin levels occurred predominantly at crypt-villus junctions, butwere also seen on the villi (FIG. 19d ). Very infrequently these lesionswere also seen near the crypt base.

The majority of the APC-deficient cells present on the villus epitheliumwere lost after 4-5 days, presumably by shedding. The remainingAPC-deficient lacZ-positive lesions/foci present within the cryptsfailed to expand over a 24 day period. A typical example of such alesion is given in FIG. 20e . No macroscopic adenomas were visible atthis stage. Strikingly, these small lesions persisted over a 180 dayperiod (FIG. 20g ), and only very rarely progressed to small adenomas,which did not expand beyond 2-3 villi (FIG. 20f, h ). This was in starkcontrast to the high frequency formation of large adenomas initiated inthe AHcre/APC^(flox/flox). mice following high-dose ß-NF induction. Thissuggested that the vast majority of adenomas in the latter mice resultedfrom loss of APC in stem cells.

In order to formally prove that transformation of intestinal stem cellsis the major route to adenoma formation, we employed ourLgr5-EGFP-ires-CreERT2 knock-in mice as a stem cell-specific Cre line toinducibly delete the foxed APC. To this end,Lgr5-EGFP-ires-CreERT2×APC^(flox/flox) mice were generated. In thesemice, the stem cell-specific Cre enzyme was activated with a single IPinjection of Tamoxifen (FIG. 21a ). Subsequent phenotypic changes in theintestine were tracked over a 2 month period. Accumulation of theWnt-effector protein ß-catenin was first observed in isolated CBC cellsat the crypt base after 3 days (FIG. 21a ). These transformed cells wereGFP-positive, confirming the targeted deletion of APC in the intestinalstem cells (FIG. 21b ). After 5 days, multiple crypts throughout theintestine were observed to harbor transformed (i.e. ß-catenin^(high))stem cells in association with highly proliferative clusters/pockets ofß-catenin^(high) cells within the transit-amplifying (TA) compartment(FIG. 21c, d ). This indicated that the Wnt-transformed stem cellsremain viable and rapidly generate an expanding population oftransformed progeny higher up the crypts. Eight days after inducing APCdeletion in the stem cells, the “pockets” of transformed cells hadcontinued to expand within the crypts and outpockets/evaginations of thecrypt epithelium and small microadenomas within the associated villusstroma became evident (FIG. 21e ). Cells with accumulated ß-catenin werenever present on the villus epithelium in these mice, demonstrating thatthe expanding transformed population were restricted to the intestinalcrypts. These observations are strikingly reminiscent of a model ofadenoma formation, in which Wnt-transformed cells expressing high levelsof the Wnt target gene EphB2 and -B3 expand within the crypt until theycome into contact with the Ephrin-positive villus epithelium^(21,22)(references 5). The resulting repulsive forces consequently dictate thatthe microadenoma can only continue to expand by invading the stroma ofthe neighbouring villus where it is shielded from the Ephrin-positivevillus epithelium.

The “outpockets” and microadenomas present in the 8 day inducedLgr5KI/APC^(flox/flox) mice continued their aggressive expansion, asevidenced by the presence of multiple large adenomas throughout theintestine 36 days after initiating stem cell transformation (FIG. 21f ).

To further investigate the hierarchy that exists between theAPC-deficient stem cells and their transformed progeny, we examinedexpression of the stem cell marker protein Lgr5-EGFP during the variousstages of adenoma formation in our model. In non-transformed stem cells,Lgr5-EGFP expression was restricted to the Crypt Base Columnar (CBC)cells (FIG. 22a ). Expression of this stem cell marker was maintainedfollowing the initial transformation of the stem cells after 3 days(FIG. 22b ) and was also clearly evident in the “pockets” of recentlyexpanded transformed progeny within the crypts after 8 days (FIG. 22c ),indicating that at least some aspect of “stemness” was conferred tothese cells. However, there was a marked down-regulation of Lgr5-EGFPexpression on the larger adenomas present in the intestines of 36-dayinduced mice, despite uniformly high ß-catenin levels throughout thetumor (FIG. 22d ). Lgr5-EGFP expression was limited to a few scatteredcells within the tumor mass (FIG. 23). These GFP-positive cells retainedthe slender, wedge-shaped morphology characteristic of the CBCintestinal stem cells. It is therefore tempting to speculate that theLgr5 expression in larger adenomas is marking a rare population of stemcells responsible for fueling their continued growth. Taken together,these data demonstrate that transformation of stem cells through loss ofApc is an extremely efficient route towards initiating intestinaladenoma formation. The kinetics of this process suggest that no furthermutations are required once both Apc alleles are lost in intestinalepithelium, which is in accordance with the tissue-tropism of Apc'stumor suppressor activity.

Example 5 Generation and Use of Antibodies Directed Against LGR5 andLGR6

Materials and Methods

Monoclonal rat antibodies were generated by Genovac (Freiburg, Germany)by intramuscular injection of rats with an expression plasmid expressingeither human Lgr5 or Lgr6. Rat B-cells were fused with mouse myelomacells. The resulting hybridomas were screened on HEK293 cells that weretransfected with human or Mouse Lgr5 or Lgr6 expression plasmids.

L8 (DNTcf4-LS174T) cells were cultured with and without Doxycycline for48 hrs. L8 cells are clonal derivatives of LS174T cells. UponDoxycycline (DOX) induction the L8 cells express a dominant negativeform of T-cell Factor 4 (DNTcf4; see Roose et al., 1999, Science 285:1923-1926). DNTcf4 turns off constitutive active Wnt pathway. Rat IgGwas used as negative isotype control. After 48 hrs cells are washed withice cold PBS and brought into suspension using 5 mM EDTA. All thefollowing steps are done at 4° C. Cells were blocked for 30 min in PBScontaining 2% BSA. Primary (1st) and Secondary (2nd) antibody reagentwere incubated subsequently for 1 hr, and washed with ice cold PBS/2%BSA. For the primary antibody staining we used undiluted hybridomasupernatant, 2nd antibody staining was done using Qdot® 655 goat F(ab′)2anti-rat IgG conjugates (H+L) (Molecular Probes/Invitrogen). Prior toanalysis propidium iodine was added to exclude dead cells in theanalysis.

Results

The specificity of some of the isolated antibodies is shown in Tables 4and 5, as tested by FACS analysis. 9G5 is a rat monoclonal antibodydirected against hLgr5. The analysis of endogenous Lgr5 expression wasdetermined in L8 cells. L8 cells are clonal derivatives of LS174T cells.Upon Doxycycline (DOX) induction, L8 cells express dominant negativeTcf4 (DNTcf4). DNTcf4 turns off constitutive active Wnt pathway. This isreflected in FIG. 24, showing FACS staining of L8 cells with 9G5antibody or IgG control antibody. After 48 hrs of DOX induction, indeeda reduction in endogenous hLgr5 protein levels was observed, as alsobecomes clear from the reduction in the fluorescent means of the peakfor the L8 cells treated with doxycycline.

This experiment was also performed with LGR5-specific antibodies 2F10,10C1 and 6C10. As shown in FIG. 26, similar results are obtained withany of these LGR5-specific antibodies.

TABLE 4 Specificity of Lgr5 antibodies. 9G5 recognize both mouse andhuman Lgr5. The colon cancer cell lines; DLD1 and SW480, LIM1863 do notshow specific staining for Lgr5. These antibodies were tested negativefor cross reactivity against mouse Lgr4, 6 and human Lgr4, and 6. L8mLgr5-293T hLgr5-293T (DNTcf4- overexpression overexpression LS174LS174) NR 1D9 − + + + NR 2F10 − + + + NR 4D11 − + + + NR 6C10 − + + + NR9B3 − + + + NR 3A4 − + + + NR 5A7 − + + + NR 6G2 − + + + NR 9G5 ++ ++ ++++ NR 2B8 − ++ ++ ++ NR 3B9 − ++ ++ ++ NR 5C8 − + + + NR 7B11 − + + +NR10C1 − + + + NR 4D6 − + + + NR 5E9 − + + + NR 8F2 − ++ ++ ++ NR10F7− + + +

TABLE 5 Specificity of Lgr6 antibodies. Antibodies 1d8 and 3d8 recognizemouse Lgr6 and hLgr5 in addition to human Lgr6. The colon cancer celllines; LS174, DLD1 and SW480 do not show specific staining for Lgr6.These antibodies were tested negative for cross reactivity against mouseLgr4, 5 and human Lgr4. Clone number 1d8 3d8 6d8 2f4 2h10 5e10hLgr5-293T + + − − − − overexpression mLgr6-293T + + − − − −overexpression hLgr6-293T ++ ++ ++ ++ + ++ overexpression LS174 − − − −− − L8 (LS174- − − − − − − DNTcf4)

Example 6 Expression Analysis of Colon and Small Intestine Derived StemCells Compared to their Direct Progeny

Materials and Methods

Isolation of GFP Positive Epithelial Cells

Freshly isolated small intestines or colons were incised along theirlength and villi (in case of small intestine) were removed by scraping.The tissue was then incubated in PBS/5 mM EDTA for 5 minutes. Gentleshaking removed remaining villi and the intestinal tissue wassubsequently incubated in PBS/EDTA for 30 minutes at 4° C. Vigorousshaking yielded free crypts which were incubated in PBS supplementedwith Trypsine (10 mg/ml) and DNAse (0.8 u/μl) for 30 minutes at 37° C.After incubation, cells were spun down, resuspended in SMEM (Invitrogen)and filtered through a 40 μM mesh. GFP-expressing cells were isolatedusing a MoFlo cell sorter (DAKO).

Microarray Analysis

RNA was isolated from the GFP^(hi) and GFP^(lo) cell fractions ofintestines from Lgr5-EGFP-ires-CreERT2 mice. 250 ng of total RNA waslabeled using low RNA Input Linear Amp kit (Agilent Technologies, PatoAlto, Calif., USA). Labeling, hybridization, and washing protocols weredone according to guidelines (Agilent Technologies, Santa Clara, Calif.,USA). Differentially labelled cRNA from GFP^(hi) and GFP^(lo) cells fromtwo different sorts (each combining three different mice) were combinedand hybridised on 4X44K Agilent Whole Mouse Genome dual colourMicroarrays (G4122F) in two dye swap experiments, resulting in fourindividual arrays. All data analyses were performed using ArrayAssist(Stratagene Inc, La Jolla, Calif., USA) and Microsoft Excel (MicrosoftCorporation, Redmond, Wash., USA). Raw signal intensities were correctedby subtracting local background. Negative values were changed by apositive value close to zero (standard deviation of the localbackground) in order to allow calculation of rations between intensitiesfor features only present in one sample (GFP^(hi) or GFP^(lo)). Datawere filtered if both (GFP^(hi) or GFP^(lo)) intensities were changed orif both intensities were less than two time the background signal andnormalized by a Loess algorithm. Statistical analysis was performed byrunning an Excel version of SAM (Significant Analysis of Microarrays)using an Excel plug-in of the software (Tusher PNAS 2001, References 6)and “one class” as the response value. Genes were considered to besignificantly enriched in GFP^(hi) cells if they had a q-value of <0.1and where present in at least 3 out of 4 arrays and the average of allfour arrays exceeded a log 2 ration of 0.6.

Results

In order to define a gene expression profile for Lgr5⁺ intestinal stemcells, we established a protocol to sort GFP-positive epithelial cellsfrom cell suspensions prepared from freshly isolated crypts ofLgr5-EGFP-ires-CreERT2 mice (see Methods). FACS analysis distinguished aGFP-high (GFP^(hi)) and a GFP-low (GFP^(lo)) population, which wetentatively identified as CBC cells and their immediatetransit-amplifying daughters, respectively (FIG. 25). A single mouseintestine routinely yielded several hundred thousand GFP^(hi) andGFP^(lo)) cells. An example of an almost pure population ofLgr5-expressing cells is provided in FIG. 25A. In order to identifynovel stem cell genes, mRNA samples of the two populations weresubjected to comparative gene expression profiling. The gene that wasmost highly enriched in the GFP^(hi) cells was, satisfactorily, the Lgr5gene itself. Multiple genes on the list (Table 6) were alreadyidentified as intestinal Wnt target genes previously, for instance inhuman colon cancer (van der Flier et al, 2007, Gastroenterology 132,628-632), which further validated the gene list. While in situhybridizations on these Wnt target genes typically confirmed high levelexpression in CBC cells, TA cells directly above the Paneth cells alsoexpressed these genes, albeit at a much lower level. As an example, FIG.25B shows the expression of Sox9, a Wnt-responsive gene (Blache et al.,2004) crucial for Paneth cell specification (Bastide et al., 2007;Mori-Akiyama et al., 2007).

DISCUSSION

In the intestine, a long-lived pool of cycling stem cells is defined byLgr5 expression, a Wnt responsive orphan G-coupled receptor (Barker etal., 2007, Nature 449, 1003-1007). These Lgr5⁺ cells have previouslybeen observed by Leblond and colleagues, who named them Crypt BaseColumnar (CBC) cells and already speculated that these CBC cellsrepresent the stem cells of the intestinal epithelium (Cheng andLeblond, 1974, Am J Anat 141, 461-79). Here, we define a minimal geneexpression profile for these CBC cells by exploiting theLgr5-EGFP-ires-CreERT2 knock-in mice for sorting, based on GFPexpression. We defined a set genes differently expressed betweenGFP^(hi) and GFP^(lo) fractions. Based on confocal images of isolatedcrypts, we tentatively identified these as CBC cells and theirdaughters, respectively. Lgr5 was found as the most differential gene inthis set, implying that its expression is strongly restricted to CBCcells. Many other genes in the signature represented previouslyidentified Wnt-dependent genes, e.g. Ascl2, CD44, Ephb3, Sox9 and Spy(van der Flier et al, 2007, Gastroenterology 132, 628-632). Given theintimate connection between Wnt signaling and the biology of stem cellsin many tissues (Reya and Clevers, 2005, Nature 434, 843-850), this wasnot surprising.

Table 6 Expression Analysis of Stem Cells and their Direct Progeny

Small intestinal (Table 6a) and colon stem cell (Table 6b) signaturebased on Lgr5 expression. GFP-positive epithelial cells from pure cryptpreparations of Lgr5-EGFP-ires-CreERT2 mice were isolated using FACSsorting. FACS analysis distinguished two populations GFP^(hi) andGFP^(lo) cells, corresponding to the CBC cells and their immediatetransit-amplifying daughters respectively. In order to identify novelstem cell genes, mRNA samples of the two populations were subjected tocomparative gene expression profiling using Agilent microarray analysis.

TABLE 6a Comparison of small intestinal stem cells with direct progenyavg log2 ratio¹ Gene name (gfp^(high)/gfp^(low)) Lgr5 2.54 Ephb3 1.38Cd44 1.15 Rnf43 1.14 Sox9 1.12 Slc12a2 0.87 Ets2 0.80 ¹Q value <0.15

TABLE 6b Comparison of colon stem cells with direct progeny avg log2ratio¹ Gene name (gfp^(high)/gfp^(low)) Lgr5 2.98 Cd44 1.47 Cdca7 1.23Ephb3 1.11 Myb 0.81 Myc 0.77 ¹Q value <0.05

Example 7 Sequence Determination of Light Chain and Heavy Chains,Including CDR Regions, of LGR5-Specific/LGR6-Specific Antibodies

Materials and Methods:

Hybridoma Sequence

The hybridomas were produced as described in the materials and methodssection of Example 5.

Hybridoma sequences were determined from Lgr5-specific and/orLgr6-specific clonal hybridoma cell lines NR 2F10 (see Table 4) and 6d8and 2f4 (see Table 5). Total RNA was isolated using Trizol reagent andcDNA generated using superscript reverse transcriptase (Promega). cDNAwas amplified using PCR primers designed to amplify the IgG antibodyFv-DNA sequences in a ‘touch-down’ PCR. PCR fragments were cloned intoeither PJET1.2 (Fermentas) or PGEM-T (Promega) cloning vectors andsubsequently sequenced using vector-specific primers on an ABIsequencer.

IgG Antibody Fc-DNA Sequence PCR Primers:

Kappa L-chain reverse primers; 25 individually synthesized oligos,pooled, representing 50 variants:

MVK-1 (SEQ ID NO: 1) GACATTGTTCTCACCCAGTCTCC MVK-2 (SEQ ID NO: 2)GACATTGTGCTSACCCAGTCTCC MVK-3 (SEQ ID NO: 3) GACATTGTGATGACTCAGTCTCCMVK-4 (SEQ ID NO: 4) GACATTGTGCTMACTCAGTCTCC MVK-5 (SEQ ID NO: 5)GACATTGTGYTRACACAGTCTCC MVK-6 (SEQ ID NO: 6) GACATTGTRATGACACAGTCTCCMVK-7 (SEQ ID NO: 7) GACATTMAGATRACCCAGTCTCC MVK-8 (SEQ ID NO: 8)GACATTGCAGATGAMCCAGTCTCC MVK-9 (SEQ ID NO: 9) GACATTCAGATGACDCAGTCTCCMVK-10 (SEQ ID NO: 10) GACATTCAGATGACACAGACTAC MVK-11 (SEQ ID NO: 11)GACATTCAGATGATTCAGTCTCC MVK-12 (SEQ ID NO: 12) GACATTGTTCTCAWCCAGTCTCCMVK-13 (SEQ ID NO: 13) GACATTGTTCTCTCCCAGTCTCC MVK-14 (SEQ ID NO: 14)GACATTGWGCTSACCCAATCTCC MVK-15 (SEQ ID NO: 15) GACATTSTGATGACCCARTCTCMVK-16 (SEQ ID NO: 16) GACATTKTGATGACCCARACTCC MVK-17 (SEQ ID NO: 17)GACATTGTGATGACTCAGGCTAC MVK-18 (SEQ ID NO: 18) GACATTGTGATGACBCAGGCTGCMVK-19 (SEQ ID NO: 19) GACATTGTGATAACYCAGGATG MVK-20 (SEQ ID NO: 20)GACATTGTGATGACCCAGTTTGC MVK-21 (SEQ ID NO: 21) GACATTGTGATGACACAACCTGCMVK-22 (SEQ ID NO: 22) GACATTGTGATGACCCAGATTCC MVK-23 (SEQ ID NO: 23)GACATTTTGCTGACTCAGTCTCC MVK-24 (SEQ ID NO: 24) GACATTGTAATGACCCAATCTCCMVK-25 (SEQ ID NO: 25) GACATTGTGATGACCCACACTCC

Kappa L-Chain Forward Primer:

mck-1 (SEQ ID NO: 26) ACACTCATTCCTGTTGAAGCTCTTGAC

H-chain variable region reverse primers, 25 individually synthesizedoligos, pooled, representing 88 variants:

MVH-1 (SEQ ID NO: 27) GCCGGCCATGGCCGAGGTRMAGCTTCAGGAGTCAGGAC MVH-2(SEQ ID NO: 28) GCCGGCCATGGCCGAGGTSCAGCTKCAGCAGTCAGGAC MVH-3(SEQ ID NO: 29) GCCGGCCATGGCCCAGGTGCAGCTGAAGSASTCAGG MVH-4(SEQ ID NO: 30) GCCGGCCATGGCCGAGGTGCAGCTTCAGGAGTCSGGAC MVH-5(SEQ ID NO: 31) GCCGGCCATGGCCGARGTCCAGCTGCAACAGTCYGGAC MVH-6(SEQ ID NO: 32) GCCGGCCATGGCCCAGGTCCAGCTKCAGCAATCTGG MVH-7(SEQ ID NO: 33) GCCGGCCATGGCCCAGSTBCAGCTGCAGCAATCTGG MVH-8(SEQ ID NO: 34) GCCGGCCATGGCCCAGGTYCAGCTGCAGCAGTCTGGRC MVH-9(SEQ ID NO: 35) GCCGGCCATGGCCCAGGTYCAGCTYCAGCAGTCTGG MVH-10(SEQ ID NO: 36) GCCGGCCATGGCCGAGGTCCARCTGCAACAATCTGGACC MVH-11(SEQ ID NO: 37) GCCGGCCATGGCCCAGGTCCACGTGAAGCAGTCTGGG MVH-12(SEQ ID NO: 38) GCCGGCCATGGCCGAGGTGAASSTGGTGGAATCTG MVH-13(SEQ ID NO: 39) GCCGGCCATGGCCGAVGTGAAGYTGGTGGAGTCTG MVH-14(SEQ ID NO: 40) GCCGGCCATGGCCGAGGTGCAGSKGGTGGAGTCTGGGG MVH-15(SEQ ID NO: 41) GCCGGCCATGGCCGAKGTGCAMCTGGTGGAGTCTGGG MVH-16(SEQ ID NO: 42) GCCGGCCATGGCCGAGGTGAAGCTGATGGARTCTGG MVH-17(SEQ ID NO: 43) GCCGGCCATGGCCGAGGTGCARCTTGTTGAGTCTGGTG MVH-18(SEQ ID NO: 44) GCCGGCCATGGCCGARGTRAAGCTTCTAGAGTCTGGA MVH-19(SEQ ID NO: 45) GCCGGCCATGGCCGAAGTGAARSTTGAGGAGTCTGG MVH-20(SEQ ID NO: 46) GCCGGCCATGGCCGAAGTGATGCTGGTGGAGTCTGGG MVH-21(SEQ ID NO: 47) GCCGGCCATGGCCCAGGTTACTCTRAAAGWGTSTGGCC MVH-22(SEQ ID NO: 48) GCCGGCCATGGCCCAGGTCCAACTVCAGCARCCTGG MVH-23(SEQ ID NO: 49) GCCGGCCATGGCCCAGGTYCARCTGCAGCAGTCTG MVH-24(SEQ ID NO: 50) GCCGGCCATGGCCGATGTGAACTTGGAAGTGTCTGG MVH-25(SEQ ID NO: 51) GCCGGCCATGGCCGAGGTGAAGGTCATCGAGTCTGG

H-Chain Forward Primers:

MJH-REV1&2 (SEQ ID NO: 64) GGGGGTGTCGTTTTGGCTGAGGAGACGGTGACCGTGGMJH-REV2INT (SEQ ID NO: 65) GGGGGTGTCGTTTTGGCTGAGGAGACGGTGACAGTGGMJH-REV3 (SEQ ID NO: 66) GGGGGTGTCGTTTTGGCTGAGGAGACGGTGACCAGAG MJH-REV4(SEQ ID NO: 67) GGGGGTGTCGTTTTGGCTGAGGAGACGGTGACCGAGG

Variable position key: R (A/G); M (A/C); Y (T/C); W (A/T); S (G/C); K(G/T); H (A/T/C); B (G/C/T); V (G/A/C); D (G/A/T); N (G/A/T/C)

In this experiment, mouse-specific oligos are used. For morereproducible results, rat-specific oligos can be used as well.

Results

The light chain sequence of LGR5-specific antibody NR 2F10 (see Table 4)and the heavy chain sequences of LGR6-specific antibodies 6d8 and 2f4(see Table 5) are depicted in FIG. 27. The CDR regions are indicated inbold and in italics. The CDR sequences were determined according toKabat (Kabat et al., “Sequences of Proteins of Immunological Interest,”U.S. Dept. of Health and Human Services, National Institute of Health,1987). Antibodies or functional equivalents thereof comprising at leastone of these CDR sequences constitute a high affinity binding compoundwith a high specificity for their target proteins LGR5 and/or LGR6.

REFERENCES 1

-   1) Reya, T., Morrison, S. J., Clarke, M. F. & Weissman, I. L. Stem    cells, cancer, and cancer stem cells. Nature 414, 105-111 (2001)-   2) Stingl J, Eirew P, Ricketson I, Shackleton M, Vaillant F, Choi D,    Li H I, Eaves C J Purification and unique properties of mammary    epithelial stem cells. Nature. 439:993-7-   3) Bach S P, Renehan A G, Potten C S. Stem cells: the intestinal    stem cell as a paradigm. Carcinogenesis 21(3):469-76 (2000)-   4) Booth C, Potten C S. Gut instincts: thoughts on intestinal    epithelial stem cells. J. Clin. Invest 105(11):1493-9 (2000)-   5) Bjerknes M, Cheng H. Clonal analysis of mouse intestinal    epithelial progenitors. Gastroenterology 116(1):7-14 (1999)-   6) Nishimura S, Wakabayashi N, Toyoda K, Kashima K, Mitsufuji S.    Expression of Musashi-1 in human normal colon crypt cells: a    possible stem cell marker of human colon epithelium. Dig. Dis. Sci.    48(8):1523-9 (2003)-   7) Potten C S, Booth C, Tudor G L, Booth D, Brady G, Hurley P,    Ashton G, Clarke R, Sakakibara S, Okano H. Identification of a    putative intestinal stem cell and early lineage marker; musashi-1.    Differentiation 71(1):28-41 (2003)-   8) He X C, Zhang J, Tong W G, Tawfik O, Ross J, Scoville D H, Tian    Q, Zeng X, He X, Wiedemann L M, Mishina Y, Li L B M P signaling    inhibits intestinal stem cell self-renewal through suppression of    Wnt-beta-catenin signaling. Nat Genet. 36:1117-21 (2004)-   9) Bjerknes M, Cheng H. Re-examination of P-PTEN staining patterns    in the intestinal crypt. Nat Genet. 37: 1016-7 (2005)-   10) Marshman E, Booth C, Potten C S. The intestinal epithelial stem    cell. Bioessays 24(1):91-8 (2002)-   11) Yatabe Y, Tavare S, Shibata D. Investigating stem cells in human    colon by using methylation patterns. Proc. Natl. Acad. Sci. USA    98(19):10839-44 (2001)-   12) Radtke, F and Clevers, H., Self-renewal and cancer of the gut:    Two sides of a coin. Review Science. 307: 1904-1909 (2005)-   13) Reya, T., Morrison, S. J., Clarke, M. F. & Weissman, I. L. Stem    cells, cancer, and cancer stem cells. Nature 414, 105-111 (2001)-   14) Clarke M F, Dick J E, Dirks P B, Eaves C J, Jamieson C H, Jones    D L, Visvader J, Weissman I L, Wahl G M. Cancer Stem    Cells—Perspectives on Current Status and Future Directions: AACR    Workshop on Cancer Stem Cells. Cancer Res. 66:9339-44 (2006).-   15) Lapidot T, Sirard C, Vormoor J, Murdoch B, Hoang T,    Caceres-Cortes J, Minden M, Paterson B, Caligiuri M A, Dick J E. A    cell initiating human acute myeloid leukaemia after transplantation    into SCID mice. Nature. 367:645-8 (1994)-   16) Bonnet D, Dick J E. Human acute myeloid leukemia is organized as    a hierarchy that originates from a primitive hematopoietic cell. Nat    Med. 3:730-7 (1997).-   17) Al-Hajj M, Wicha M S, Benito-Hernandez A, Morrison S J, Clarke    M F. Prospective identification of tumorigenic breast cancer cells.    Proc Natl Acad Sci USA. 100:3983-8 (2003).-   18) Nakano I, Kornblum H I Brain tumor stem cells. Pediatr Res.    59:54R-8R. Review (2006)-   19) Collins A T, Maitland N J. Prostate cancer stem cells. Eur J    Cancer. 42:1213-8. Review (2006)-   20) O'Brien C A, Pollett A, Gallinger S, Dick J E A human colon    cancer cell capable of initiating tumour growth in immunodeficient    mice. Nature 445:106-10 (2007).-   21) Ricci-Vitiani L, Lombardi D G, Pilozzi E, Biffoni M, Todaro M,    Peschle C, De Maria R. Identification and expansion of human    colon-cancer-initiating cells. Nature. 445:111-5 (2007)-   22) van de Wetering, M., Sancho, E., Verweij, C., de Lau, W., Oving,    I., Hurlstone, A., van der Horn, K., Batlle, E., Coudreuse, D.,    Haramis, A-P., Tjon-Pon-Fong, M., Moerer, P., van den Born, M.,    Soete, G., Pals, S., Eilers, M., Medema, R., Clevers, H. The    beta-catenin/TCF4 complex imposes a crypt progenitor phenotype on    colorectal cancer cells. Cell 111: 241-250 (2002)-   23) Wielenga, V. J., Smits, R., Korinek, V., Smit, L., Kielman, M.,    Fodde, R., Clevers, H., Pals, S. T. Expression of CD44 in Apc and    Tcf mutant mice implies regulation by the WNT pathway. Am J Pathol    54: 515-523 (1999)-   24) Malaterre, J. et al. c-Myb is required for progenitor cell    homeostasis in colonic crypts. Proc. Natl. Acad. Sci USA 104,    3829-3834 (2007)-   25) Brigelius-Flohe, R. Glutathione peroxidases and redox-regulated    transcription factors (2006) Biological Chemistry, 387 (10-11), pp.    1329-1335.-   26) Neid, M., Wittekind, C. Epidemiology, pathology, and staging of    mesenchymal and endocrine tumours of the gastrointestinal    tract (2007) Chirurgische Gastroenterologie nterdisziplinar, 23 (2),    pp. 108-112.-   27) Battle, E., Henderson, J. T., Beghtel, H., van den Born, M.,    Sancho, E., Huls, G., Meeldijk, J., Robertson, J., van de Wetering,    M., Pawson, T., Clevers, H. Beta-catenin and TCF mediate cell    positioning in the intestinal epithelium by controlling the    expression of EphB/ephrinB. Cell 111: 251-263 (2002)-   28) Haramis, A. P., Begthel, H., van den Born, M., van Es, J.,    Jonkheer, S., Offerhaus, G. J., Clevers, H. De novo crypt formation    and Juvenile Polyposis upon BMP inhibition Science. 303: 1684-1686    (2004)-   29) Hewitt, K. J., Agarwal, R., Morin, P. J. The claudin gene    family: Expression in normal and neoplastic tissues (2006) BMC    Cancer, 6, art. no. 186-   30) Shea Yu Hsu, Kudo, M., Chen, T., Nakabayashi, K., Bhalla, A.,    Van der Spek, P. J., Van Duin, M., ( . . . ), Hsueh, A. J. W. The    three subfamilies of leucine-rich repeat-containing G    protein-coupled receptors (LGR): Identification of LGR6 and LGR7 and    the signaling mechanism for LGR7 (2000) Molecular Endocrinology, 14    (8), pp. 1257-1271.-   31) Van Schoore, G., Mendive, F., Pochet, R., Vassart, G. Expression    pattern of the orphan receptor LGR4/GPR48 gene in the mouse (2005)    Histochemistry and Cell Biology, 124 (1), pp. 35-50-   32) Mazerbourg, S., Bouley, D. M., Sudo, S., Klein, C. A., Zhang, J.    V., Kawamura, K., Goodrich, L. V., ( . . . ), Hsueh, A. J. W.    Leucine-rich repeat-containing, G protein-coupled receptor 4 null    mice exhibit intrauterine growth retardation associated with    embryonic and perinatal lethality. (2004) Molecular Endocrinology,    18 (9), pp. 2241-2254-   33) Mendive, F., Laurent, P., Van Schoore, G., Skarnes, W., Pochet,    R., Vassart, G. Defective postnatal development of the male    reproductive tract in LGR4 knockout mice. 2006) Developmental    Biology, 290 (2), pp. 421-434.-   34) Kato, S., Matsubara, M., Matsuo, T., Mohri, Y., Kazama, I.,    Hatano, R., Umezawa, A., ( . . . ), Nishimori, K. Leucine-rich    repeat-containing G protein-coupled receptor-4 (LGR4, Gpr48) is    essential for renal development in mice (2006) Nephron—Experimental    Nephrology, 104 (2), pp. e63-e75-   35) Morita H, Mazerbourg S, Bouley D M, Luo C W, Kawamura K,    Kuwabara Y, Baribault H, Tian H, Hsueh A J. Neonatal lethality of    LGR5 null mice is associated with ankyloglossia and gastrointestinal    distension. Mol Cell Biol. 24:9736-43 (2004)-   36) Yamamoto Y, Sakamoto M, Fujii G, Tsuiji H, Kenetaka K, Asaka M,    Hirohashi S. Overexpression of orphan G-protein-coupled receptor,    Gpr49, in human hepatocellular carcinomas with beta-catenin    mutations. Hepatology. 37:528-33 (2003)-   37) McClanahan T, Koseoglu S, Smith K, Grein J, Gustafson E, Black    S, Kirschmeier P, Samatar A A. Identification of overexpression of    orphan G protein-coupled receptor GPR49 in human colon and ovarian    primary tumors. Cancer Biol Ther. 5:419-26. (2006).

REFERENCES 2

-   1. Gregorieff, A. & Clevers, H. Wnt signaling in the intestinal    epithelium: from endoderm to cancer. Genes Dev 19, 877-90 (2005).-   2. Bjerknes, M. & Cheng, H. Clonal analysis of mouse intestinal    epithelial progenitors. Gastroenterology 116, 7-14 (1999).-   3. Winton, D. J. & Ponder, B. A. Stem-cell organization in mouse    small intestine. Proc Biol Sci 241, 13-8 (1990).-   4. Potten, C. S., Booth, C. & Pritchard, D. M. The intestinal    epithelial stem cell: the mucosal governor. Int J Exp Pathol 78,    219-43 (1997).-   5. Korinek, V. et al. Depletion of epithelial stem-cell compartments    in the small intestine of mice lacking Tcf-4. Nat Genet 19, 379-83    (1998).-   6. van de Wetering, M. et al. The beta-catenin/TCF-4 complex imposes    a crypt progenitor phenotype on colorectal cancer cells. Cell 111,    241-50 (2002).-   7. Van der Flier, L. G. et al. The Intestinal Wnt/TCF Signature.    Gastroenterology 132, 628-32 (2007).-   8. Hsu, S. Y., Liang, S. G. & Hsueh, A. J. Characterization of two    LGR genes homologous to gonadotropin and thyrotropin receptors with    extracellular leucine-rich repeats and a G protein-coupled,    seven-transmembrane region. Mol Endocrinol 12, 1830-45 (1998).-   9. McClanahan, T. et al. Identification of overexpression of orphan    G protein-coupled receptor GPR49 in human colon and ovarian primary    tumors. Cancer Biol Ther 5, 419-26 (2006).-   10. Yamamoto, Y. et al. Overexpression of orphan G-protein-coupled    receptor, Gpr49, in human hepatocellular carcinomas with    beta-catenin mutations. Hepatology 37, 528-33 (2003).-   11. Morita, H. et al. Neonatal lethality of LGR5 null mice is    associated with ankyloglossia and gastrointestinal distension. Mol    Cell Biol 24, 9736-43 (2004).-   12. Reya, T. & Clevers, H. Wnt signalling in stem cells and cancer.    Nature 434, 843-50 (2005).-   13. Cheng, H. & Leblond, C. P. Origin, differentiation and renewal    of the four main epithelial cell types in the mouse small    intestine. V. Unitarian Theory of the origin of the four epithelial    cell types. Am J Anat 141, 537-61 (1974).-   14. Bjerknes, M. & Cheng, H. The stem-cell zone of the small    intestinal epithelium. III. Evidence from columnar, enteroendocrine,    and mucous cells in the adult mouse. Am J Anat 160, 77-91 (1981).-   15. Stappenbeck, T. S., Mills, J. C. & Gordon, J. I. Molecular    features of adult mouse small intestinal epithelial progenitors.    Proc Natl Acad Sci USA 100, 1004-9 (2003).-   16. Soriano, P. Generalized lacZ expression with the ROSA26 Cre    reporter strain. Nat Genet 21, 70-1 (1999).-   17. Potten, C. S., Owen, G. & Booth, D. Intestinal stem cells    protect their genome by selective segregation of template DNA    strands. J Cell Sci 115, 2381-8 (2002).-   18. Ohlstein, B., Kai, T., Decotto, E. & Spradling, A. The stem cell    niche: theme and variations. Curr Opin Cell Biol 16, 693-9 (2004).-   19. Clayton, E. et al. A single type of progenitor cell maintains    normal epidermis. Nature 446, 185-9 (2007).-   20. Nishimura, S., Wakabayashi, N., Toyoda, K., Kashima, K. &    Mitsufuji, S. Expression of Musashi-1 in human normal colon crypt    cells: a possible stem cell marker of human colon epithelium. Dig    Dis Sci 48, 1523-9 (2003).-   21. Potten, C. S. et al. Identification of a putative intestinal    stem cell and early lineage marker; musashi-1. Differentiation 71,    28-41 (2003).-   22. O'Brien, C. A., Pollett, A., Gallinger, S. & Dick, J. E. A human    colon cancer cell capable of initiating tumour growth in    immunodeficient mice. Nature 445, 106-10 (2007).-   23. He, X. C. et al. BMP signaling inhibits intestinal stem cell    self-renewal through suppression of Wnt-beta-catenin signaling. Nat    Genet 36, 1117-21 (2004).-   24. Claudinot, S., Nicolas, M., Oshima, H., Rochat, A. &    Barrandon, Y. Long-term renewal of hair follicles from clonogenic    multipotent stem cells. Proc Natl Acad Sci USA 102, 14677-82 (2005).-   25. Cotsarelis, G., Sun, T. T. & Lavker, R. M. Label-retaining cells    reside in the bulge area of pilosebaceous unit: implications for    follicular stem cells, hair cycle, and skin carcinogenesis. Cell 61,    1329-37 (1990).-   26. Tumbar, T. et al. Defining the epithelial stem cell niche in    skin. Science 303, 359-63 (2004).-   27. Morris, R. J. et al. Capturing and profiling adult hair follicle    stem cells. Nat Biotechnol 22, 411-7 (2004).-   28. Bjerknes, M. & Cheng, H. Multipotential stem cells in adult    mouse gastric epithelium. Am J Physiol Gastrointest Liver Physiol    283, G767-77 (2002).-   29. Sleeman, K. E. et al. Dissociation of estrogen receptor    expression and in vivo stem cell activity in the mammary gland. J    Cell Biol 176, 19-26 (2007).-   30. Muncan, V. et al. Rapid loss of intestinal crypts upon    conditional deletion of the Wnt/Tcf-4 target gene c-Myc. Mol Cell    Biol 26, 8418-26 (2006).

REFERENCES 5

-   1. Barker, N. v. d. W., M. Clevers, H. The intestinal stem cell. Gen    Dev in press, (2008).-   2. Potten, C. S. Kinetics and possible regulation of crypt cell    populations under normal and stress conditions. Bull Cancer 62,    419-30 (1975).-   3. Barker, N. et al. Identification of stem cells in small intestine    and colon by marker gene Lgr5. Nature 449, 1003-7 (2007).-   4. Cheng, H. & Leblond, C. P. Origin, differentiation and renewal of    the four main epithelial cell types in the mouse small intestine. V.    Unitarian Theory of the origin of the four epithelial cell types. Am    J Anat 141, 537-61 (1974).-   5. Cheng, H. & Leblond, C. P. Origin, differentiation and renewal of    the four main epithelial cell types in the mouse small intestine. I.    Columnar cell. Am J Anat 141, 461-79 (1974).-   6. Marshman, E., Booth, C. & Potten, C. S. The intestinal epithelial    stem cell. Bioessays 24, 91-8 (2002).-   7. Bjerknes, M. & Cheng, H. The stem-cell zone of the small    intestinal epithelium. II. Evidence from paneth cells in the newborn    mouse. Am J Anat 160, 65-75 (1981).-   8. Bjerknes, M. & Cheng, H. The stem-cell zone of the small    intestinal epithelium. I. Evidence from Paneth cells in the adult    mouse. Am J Anat 160, 51-63 (1981).-   9. Ireland, H., Houghton, C., Howard, L. & Winton, D. J. Cellular    inheritance of a Cre-activated reporter gene to determine Paneth    cell longevity in the murine small intestine. Dev Dyn 233, 1332-6    (2005).-   10. Jones, S. et al. Comparative lesion sequencing provides insights    into tumor evolution. Proc Natl Acad Sci USA 105, 4283-8 (2008).-   11. Kinzler, K. W. & Vogelstein, B. Lessons from hereditary    colorectal cancer. Cell 87, 159-70 (1996).-   12. Korinek, V. et al. Constitutive transcriptional activation by a    beta-catenin-Tcf complex in APC−/−colon carcinoma. Science 275,    1784-7 (1997).-   13. Morin, P. J. et al. Activation of beta-catenin-Tcf signaling in    colon cancer by mutations in beta-catenin or APC. Science 275,    1787-90 (1997).-   14. van de Wetering, M. et al. The beta-catenin/TCF-4 complex    imposes a crypt progenitor phenotype on colorectal cancer cells.    Cell 111, 241-50 (2002).-   15. Van der Flier, L. G. et al. The Intestinal Wnt/TCF Signature.    Gastroenterology 132, 628-32 (2007).-   16. Sansom, O. J. et al. Loss of Apc in vivo immediately perturbs    Wnt signaling, differentiation, and migration. Genes Dev 18, 1385-90    (2004).-   17. Shibata, H. et al. Rapid colorectal adenoma formation initiated    by conditional targeting of the Apc gene. Science 278, 120-3 (1997).-   18. Sansom, O. J. et al. Myc deletion rescues Apc deficiency in the    small intestine. Nature 446, 676-9 (2007).-   19. Sansom, O. J. et al. Cyclin D1 is not an immediate target of    beta-catenin following Apc loss in the intestine. J Biol Chem 280,    28463-7 (2005).-   20. Soriano, P. Generalized lacZ expression with the ROSA26 Cre    reporter strain. Nat Genet 21, 70-1 (1999).

The invention claimed is:
 1. A method for testing the effect of acompound comprising (a) contacting a cell population comprising cancerstem cells in vitro with said compound, wherein the cancer stem cellscomprise Lgr6 and/or Lgr5 embedded in their cell membrane; and (b)testing the ability of said contacted cancer stem cells to generate atumor relative to cancer stem cells that are not contacted with saidcompound, wherein a difference in the tumor-generating ability of thecontacted and non-contacted cancer stem cells indicates an effect of thecompound.
 2. The method of claim 1, further comprising testing theeffect of said compound on normal tissue stem cells or organ stem cells,comprising contacting normal tissue stem cells or organ stem cells withsaid compound and determining a change in the number of normal tissuestem cells or organ stem cells, following contact with said compound. 3.The method of claim 1, wherein the cell population comprises at least50% Lgr5 and/or Lgr6 positive stem cells, at least 60% Lgr5 and/or Lgr6positive stem cells, at least 70% Lgr5 and/or Lgr6 positive stem cells,at least 80% Lgr5 and/or Lgr6 positive stem cells, at least 90% Lgr5and/or Lgr6 positive stem cells, or at least 95% Lgr5 and/or Lgr6positive stem cells.
 4. The method of claim 1, wherein said compound isan anti-Lgr5 antibody.
 5. The method of claim 1, further comprisingmeasuring the number of cancer stem cells in the cell population beforeand after contact with said compound.
 6. The method of claim 1, furthercomprising, prior to step (a), obtaining the cell population comprisingcancer stem cells by contacting a cell suspension prepared from a solidor liquid tumor sample with an Lgr6 specific antibody or antibodyfragment, and isolating cells that bind to the Lgr6 specific antibody orantibody fragment.